> **Summary of the MAQC Data Sets**
>
> **The MicroArray Quality Control (MAQC) Consortium**

Contact:

*Leming Shi,* National Center for Toxicological Research (NCTR), U.S.
Food and Drug Administration (FDA) 3900 NCTR Road, Jefferson, Arkansas
72079, U.S.A. Tel: +1-870-543-7387, Fax: +1-870-543-7854

[[Leming.Shi@fda.hhs.gov]{.underline}](mailto:Leming.Shi@fda.hhs.gov);
[[http://edkb.fda.gov/MAQC/;]{.underline}](http://edkb.fda.gov/MAQC/;)
[[http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/]{.underline}](http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/)

> September 12, 2006, 9:26 AM CDT

1.  Results of the MAQC project has been described in a series of
    manuscripts published in *Nature Biotechnology,* September 8, 2006.
    PDF files of the manuscripts are freely available at
    [[http://www.nature.com/nbt/focus/maqc/.]{.underline}](http://www.nature.com/nbt/focus/maqc/.)

2.  The MAQC data set are publicly available starting through the
    following four mechanisms:

-   GEO (series accession number: **GSE5350);**

```{=html}
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```
-   ArrayExpress (accession number: **E-TABM-132,** pending);

```{=html}
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```
-   ArrayTrack
    [(<http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/);>]{.underline}
    and

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```
-   The MAQC website
    [(<http://edkb.fda.gov/MAQC/MainStudy/upload/)>]{.underline} -- a
    good place to download normalized data in a table format (see Table
    8 of this document).

3.  Image files (e.g., .DAT files from Affymetrix platform) are not
    publicly deposited, but will be made available upon request.

4.  For updated information (e.g., corrections, detailed data set
    annotation, and feedback from users) about the MAQC data sets,
    please visit the MAQC website
    [(<http://edkb.fda.gov/MAQC/).>]{.underline}

> 5\. Corrections, questions, and comments should be addressed to
> [[Leming.Shi@fda.hhs.gov]{.underline}](mailto:Leming.Shi@fda.hhs.gov).
>
> The total number of microarrays used in the MAQC project: **1,329**

**Table 1. *"Official"* Platforms and Data Included in the MAQC Main
Study: 573 microarrays^\*^\
**(Eight microarray platforms and three alternative platforms)

<table>
<colgroup>
<col style="width: 10%" />
<col style="width: 5%" />
<col style="width: 9%" />
<col style="width: 8%" />
<col style="width: 7%" />
<col style="width: 7%" />
<col style="width: 9%" />
<col style="width: 10%" />
<col style="width: 6%" />
<col style="width: 6%" />
<col style="width: 8%" />
<col style="width: 9%" />
</colgroup>
<tbody>
<tr class="odd">
<td><strong>Manufacturer</strong></td>
<td><strong>Code</strong></td>
<td><strong>Protocol</strong></td>
<td><strong>Platform</strong></td>
<td><p><strong>GEO</strong></p>
<p><strong>GPL#</strong></p></td>
<td><p><strong>Array</strong></p>
<p><strong>Express#</strong></p></td>
<td><p><strong>ArrayTrack</strong></p>
<p><strong>Experiments</strong></p></td>
<td><p><strong>Number of</strong></p>
<p><strong>Probes</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of Test</strong></p>
<p><strong>Sites</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of</strong></p>
<p><strong>Samples</strong></p></td>
<td><blockquote>
<p><strong>Number</strong></p>
<p><strong>of</strong></p>
<p><strong>Replicates</strong></p>
</blockquote></td>
<td><p><strong>Total</strong></p>
<p><strong>Number of</strong></p>
<p><strong>Microarrays</strong></p></td>
</tr>
<tr class="even">
<td><p>Applied</p>
<p>Biosystems</p></td>
<td>ABI</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>Human</p>
<p>Genome</p>
<p>Survey</p>
<p>Microarray</p>
<p>v2.0</p></td>
<td>GPL2986</td>
<td><p><strong>A-</strong></p>
<p><strong>MEXP-</strong></p>
<p><strong>503</strong></p></td>
<td><p>ABI_1</p>
<p>ABI_2</p>
<p>ABI_3</p></td>
<td>32,878</td>
<td>3</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>60</td>
</tr>
<tr class="odd">
<td>Affymetrix</td>
<td>AFX</td>
<td><p>One-Color</p>
<p>Microarra y</p></td>
<td><p>HG-U133</p>
<p>Plus 2.0</p>
<p>GeneChip®</p></td>
<td>GPL570</td>
<td><p><strong>A‑</strong></p>
<p><strong>AFFY-</strong></p>
<p><strong>44</strong></p></td>
<td><p>AFX_1</p>
<p>AFX_2</p>
<p>AFX_3</p>
<p>AFX_4</p>
<p>AFX_5</p>
<p>AFX_6</p></td>
<td>54,675</td>
<td>6</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>120</td>
</tr>
<tr class="even">
<td rowspan="2">Agilent</td>
<td>AGL</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td rowspan="2"><p>Whole</p>
<p>Human</p>
<p>Genome</p>
<p>Oligo</p>
<p>Microarray,</p>
<p>G4112A</p></td>
<td rowspan="2">GPL1708</td>
<td rowspan="2"><p><strong>A-</strong></p>
<p><strong>AGIL-</strong></p>
<p><strong>11</strong></p></td>
<td><p>AGL_1</p>
<p>AGL_2</p>
<p>AGL_3</p></td>
<td rowspan="2"><p>43 ,931</p>
<p>(same</p>
<p>printing;</p>
<p>41058 –</p>
<p>GeneSpring <sup>d</sup> )</p></td>
<td>3</td>
<td>2</td>
<td><blockquote>
<p>10</p>
</blockquote></td>
<td>60</td>
</tr>
<tr class="odd">
<td>AG1</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>AG1_1</p>
<p>AG1_2</p>
<p>AG1_3</p></td>
<td>3</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>60</td>
</tr>
<tr class="even">
<td>Eppendorf</td>
<td>EPP</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>DualChip®</p>
<p>Microarray</p></td>
<td>GPL4096</td>
<td></td>
<td><p>EPP_1</p>
<p>EPP_2</p>
<p>EPP_3</p></td>
<td>294</td>
<td>3</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>60</td>
</tr>
<tr class="odd">
<td>GE Healthcare</td>
<td>GEH</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>CodeLink<sup>™</sup></p>
<p>Human</p>
<p>Whole</p>
<p>Genome</p></td>
<td>GPL2895</td>
<td><p><strong>A‑</strong></p>
<p><strong>GEHB-</strong></p>
<p><strong>1</strong></p></td>
<td><p>GEH_1</p>
<p>GEH_2</p>
<p>GEH_3</p>
<p>GEH_2Fail</p></td>
<td>54,359</td>
<td><sub>3</sub>a</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>80</td>
</tr>
<tr class="even">
<td>Illumina</td>
<td>ILM</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>Human-6</p>
<p>BeadChip,</p>
<p>48K v1.0</p></td>
<td>GPL2507</td>
<td><p><strong>A-</strong></p>
<p><strong>MEXP-</strong></p>
<p><strong>524</strong></p></td>
<td><p>ILM_1</p>
<p>ILM_2</p>
<p>ILM_3</p></td>
<td>47,293</td>
<td><sub>3</sub>b</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>59</td>
</tr>
<tr class="odd">
<td>NCI_Operon</td>
<td>NCI</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td><p>Operon</p>
<p>Human</p>
<p>Oligo Set</p>
<p>v3</p></td>
<td>GPL4108</td>
<td></td>
<td><p>NCI_1</p>
<p>NCI_2</p>
<p>NCI_2Fail</p>
<p>NCI_3Fail</p></td>
<td>37,632</td>
<td><sub>3</sub>c</td>
<td>4</td>
<td><blockquote>
<p>5</p>
</blockquote></td>
<td>74</td>
</tr>
<tr class="even">
<td><p><em>Applied</em></p>
<p><em>Biosystems</em></p></td>
<td><em>TAQ</em></td>
<td><p><em>TaqMan®</em></p>
<p><em>Assays</em></p></td>
<td><p><em>&gt;200, 000</em></p>
<p><em>assays</em></p>
<p><em>available</em></p></td>
<td><em>GPL4097</em></td>
<td></td>
<td><em>TAQ_1</em></td>
<td><em>1,004</em></td>
<td><em>1</em></td>
<td><em>4</em></td>
<td><blockquote>
<p><em>4</em></p>
</blockquote></td>
<td><p><em>N/A</em></p>
<p><em>(16)</em></p></td>
</tr>
<tr class="odd">
<td><em>Panomics</em></td>
<td><em>QGN</em></td>
<td><p><em>QuantiGene®</em></p>
<p><em>Assays</em></p></td>
<td><p><em>~2, 600</em></p>
<p><em>assays</em></p>
<p><em>available</em></p></td>
<td><em>GPL4098</em></td>
<td></td>
<td><em>QGN_1</em></td>
<td><em>245</em></td>
<td><em>1</em></td>
<td><em>4</em></td>
<td><blockquote>
<p><em>3</em></p>
</blockquote></td>
<td><p><em>N/A</em></p>
<p><em>(12)</em></p></td>
</tr>
<tr class="even">
<td><em>Gene Express</em></td>
<td><em>GEX</em></td>
<td><p><em>StaRT-PCR<sup>™</sup></em></p>
<p><em>Assa y s</em></p></td>
<td><p><em>~1, 000</em></p>
<p><em>assays</em></p>
<p><em>available</em></p></td>
<td><em>GPL4198</em></td>
<td></td>
<td><em>GEX_1</em></td>
<td><em>207</em></td>
<td><em>1</em></td>
<td><em>4</em></td>
<td><blockquote>
<p><em>3</em></p>
</blockquote></td>
<td><p><em>N/A</em></p>
<p><em>(12)</em></p></td>
</tr>
<tr class="odd">
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td><strong>573</strong></td>
</tr>
</tbody>
</table>

> *^\*^There are 40 "virtual" microarrays corresponding to the three
> alternative platforms (TAQ, QGN, and GEX).*
>
> Test sites and sample types are referenced using the following
> nomenclature: "platform code_test site\_ sample ID". Sample A = 100%
> UHRR; Sample B = 100% HBRR; Sample C = 75% UHRR:25%
>
> HBRR; and Sample D = 25% UHRR:75% HBRR.
>
> ^a^Test site GEH_2 repeated an initial, failed experiment (GEH_2Fail,
> due to protocol issues). ^b^Test site ILM_1 only had 19 microarrays.

^c^Test site NCI_2 partially repeated an initial, failed experiment
(NCI_2Fail, due to protocol issues) with 14 microarrays. Test site NCI_3
failed an initial experiment (NCI_3Fail, due to protocol issues)

> and partially repeated the study with another batch of printed slides
> (site NCI_3r in Table 2).
>
> ^d^Data from replicating spots were averaged within GeneSpring
> software to generate a single value for each unique probe.

**Table 2. *"Additional"* Platforms and Data Included in the MAQC Main
Study: 130 microarrays\
**(Seven microarray platforms)

<table>
<colgroup>
<col style="width: 8%" />
<col style="width: 5%" />
<col style="width: 7%" />
<col style="width: 7%" />
<col style="width: 7%" />
<col style="width: 8%" />
<col style="width: 7%" />
<col style="width: 18%" />
<col style="width: 7%" />
<col style="width: 8%" />
<col style="width: 9%" />
</colgroup>
<tbody>
<tr class="odd">
<td><strong>Platform</strong></td>
<td><strong>Code</strong></td>
<td><strong>Protocol</strong></td>
<td><strong>GEO GPL#</strong></td>
<td><p><strong>Array</strong></p>
<p><strong>Express#</strong></p></td>
<td><p><strong>ArrayTrack</strong></p>
<p><strong>Experiments</strong></p></td>
<td><p><strong>Number of</strong></p>
<p><strong>Probes</strong></p></td>
<td><blockquote>
<p><strong>Test Sites</strong></p>
</blockquote></td>
<td><p><strong>Number of</strong></p>
<p><strong>Samples</strong></p></td>
<td><p><strong>Number of</strong></p>
<p><strong>Replicates</strong></p></td>
<td><p><strong>Number of</strong></p>
<p><strong>Microarrays</strong></p>
<p><strong>Per Test Site</strong></p></td>
</tr>
<tr class="even">
<td rowspan="2"><p>NCI_Operon</p>
<p>(2<sup>nd</sup> printing)</p></td>
<td rowspan="2">NCI</td>
<td rowspan="2"><p>Two-Color</p>
<p>Microarray</p></td>
<td rowspan="2">GPL4185</td>
<td rowspan="2"></td>
<td rowspan="2"><p>NCI_4</p>
<p>NCI_3r</p></td>
<td rowspan="2">36,288</td>
<td><blockquote>
<p>NCI_4: Harvard University</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="odd">
<td><blockquote>
<p>NCI_3r: FDA/CBER (repeat)</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td rowspan="2"><p>CapitalBio_</p>
<p>Operon</p></td>
<td>BIO</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td rowspan="2">GPL4187</td>
<td></td>
<td>BIO_1</td>
<td rowspan="2"><p>23,232</p>
<p>(same</p>
<p>printing)</p></td>
<td><blockquote>
<p>BIO_1: CapitalBio</p>
</blockquote></td>
<td>2</td>
<td>10</td>
<td>20</td>
</tr>
<tr class="odd">
<td>BIO1</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td></td>
<td>BIO1_1</td>
<td><blockquote>
<p>BIO1_1: CapitalBio</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td><p>Operon_</p>
<p>Operon</p></td>
<td>OPN</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td>GPL4188</td>
<td></td>
<td>OPN_1</td>
<td>37,584</td>
<td><blockquote>
<p>OPN_1: Operon</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="odd">
<td><p>NMC_</p>
<p>Operon</p></td>
<td>NMC</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td>GPL4186</td>
<td></td>
<td>NMC_1</td>
<td>36,288</td>
<td><blockquote>
<p>NMC_1: Norwegian Microarray</p>
<p>Consortium</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td rowspan="4">TeleChem</td>
<td>H25K</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td rowspan="4">GPL4219</td>
<td></td>
<td>H25K_2</td>
<td rowspan="4"><p>27,648</p>
<p>(same</p>
<p>printing)</p></td>
<td><blockquote>
<p>H25K_2: Yale University</p>
</blockquote></td>
<td>2</td>
<td>15</td>
<td>30</td>
</tr>
<tr class="odd">
<td rowspan="3">H25K1</td>
<td rowspan="3"><p>One-Color</p>
<p>Microarray</p></td>
<td rowspan="3"></td>
<td rowspan="3"><p>H25K1_1</p>
<p>H25K1_2</p>
<p>H25K1_3</p></td>
<td><blockquote>
<p>H25K1_1: TeleChem</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td><blockquote>
<p>H25K1_2: Yale University</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="odd">
<td><blockquote>
<p>H25K1_3: Wake Forest University</p>
</blockquote></td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td><strong>130</strong></td>
</tr>
</tbody>
</table>

**Table 3. *"Tumor"* Data Included in the MAQC Study: 20
microarrays**^a^**\
**(One microarray platform at two laboratories in Stanford University)

<table>
<colgroup>
<col style="width: 10%" />
<col style="width: 5%" />
<col style="width: 9%" />
<col style="width: 8%" />
<col style="width: 6%" />
<col style="width: 7%" />
<col style="width: 10%" />
<col style="width: 10%" />
<col style="width: 6%" />
<col style="width: 6%" />
<col style="width: 8%" />
<col style="width: 9%" />
</colgroup>
<tbody>
<tr class="odd">
<td><strong>Manufacturer</strong></td>
<td><strong>Code</strong></td>
<td><strong>Protocol</strong></td>
<td><strong>Platform</strong></td>
<td><p><strong>GEO</strong></p>
<p><strong>GPL#</strong></p></td>
<td><p><strong>Array</strong></p>
<p><strong>Express#</strong></p></td>
<td><p><strong>ArrayTrack</strong></p>
<p><strong>Experiments*</strong></p></td>
<td><p><strong>Number of</strong></p>
<p><strong>Probes</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of Test</strong></p>
<p><strong>Sites</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of</strong></p>
<p><strong>Samples</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of</strong></p>
<p><strong>Replicates</strong></p></td>
<td><p><strong>Total</strong></p>
<p><strong>Number of</strong></p>
<p><strong>Microarrays</strong></p></td>
</tr>
<tr class="even">
<td>Affymetrix</td>
<td>AFX</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>HG-U133</p>
<p>Plus 2.0</p>
<p>GeneChip®</p></td>
<td>GPL570</td>
<td><p><strong>A‑</strong></p>
<p><strong>AFFY-</strong></p>
<p><strong>44</strong></p></td>
<td><p>AFX_1</p>
<p>AFX _2</p></td>
<td>54,675</td>
<td>2</td>
<td>2</td>
<td>5</td>
<td><strong>20</strong></td>
</tr>
</tbody>
</table>

> ^a^Tumor_Stanford_Lab1 and Tumor_Stanford_Lab2. T = Tumor (colon
> adenocarcinoma), N = Normal (normal colon tissue, patient matched).
> The tumor data set was analyzed in Lin, G., He, X., Ji H., Shi, L.,
> Davis, R.W. and Zhong, S. *Nature Biotechnology,* **24(10),** 2006.

**Table 4. "Rat *Toxicogenomics"* Validation Data Included in the MAQC
Study: 180 microarrays\
**(Four microarray platforms in five laboratories)

<table>
<colgroup>
<col style="width: 10%" />
<col style="width: 5%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 8%" />
<col style="width: 9%" />
<col style="width: 7%" />
<col style="width: 7%" />
<col style="width: 8%" />
<col style="width: 9%" />
</colgroup>
<tbody>
<tr class="odd">
<td><strong>Manufacturer</strong></td>
<td><strong>Code</strong></td>
<td><strong>Protocol</strong></td>
<td><strong>Platform</strong></td>
<td><strong>GEO GPL#</strong></td>
<td><p><strong>Array</strong></p>
<p><strong>Express#</strong></p></td>
<td><p><strong>ArrayTrack</strong></p>
<p><strong>Experiments</strong></p></td>
<td><p><strong>Number of</strong></p>
<p><strong>Probes</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of Test</strong></p>
<p><strong>Sites</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of</strong></p>
<p><strong>Samples</strong></p></td>
<td><p><strong>Number</strong></p>
<p><strong>of</strong></p>
<p><strong>Replicates</strong></p></td>
<td><p><strong>Total</strong></p>
<p><strong>Number of</strong></p>
<p><strong>Microarrays</strong></p></td>
</tr>
<tr class="even">
<td><p>Applied</p>
<p>Biosystems</p></td>
<td>ABI</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>Rat Genome</p>
<p>Survey</p>
<p>Microarray</p></td>
<td>GPL2996</td>
<td></td>
<td>ABI</td>
<td>26,857</td>
<td>1</td>
<td>6</td>
<td>6</td>
<td>36</td>
</tr>
<tr class="odd">
<td>Affymetrix</td>
<td>AFX</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>Rat Genome</p>
<p>230 2.0</p>
<p>GeneChip®</p></td>
<td>GPL1355</td>
<td><p><strong>A-AFFY-</strong></p>
<p><strong>43</strong></p></td>
<td><p>AFX</p>
<p>AFX2</p></td>
<td>31,099</td>
<td>2</td>
<td>6</td>
<td>6</td>
<td>72</td>
</tr>
<tr class="even">
<td>Agilent</td>
<td>AG1</td>
<td><p>One-Color</p>
<p>Microarra y</p></td>
<td><p>Whole</p>
<p>Rat Genome</p>
<p>Oligo</p>
<p>Microarray,</p>
<p>G4131A</p></td>
<td>GPL2877</td>
<td><p><strong>A-AGIL‑</strong></p>
<p><strong>19</strong></p></td>
<td>AG1</td>
<td><p>43,628</p>
<p>(41,070 –</p>
<p>GeneSpring<sup>a</sup>)</p></td>
<td>1</td>
<td>6</td>
<td>6</td>
<td>36</td>
</tr>
<tr class="odd">
<td>GE Healthcare</td>
<td>GEH</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>Rat Whole</p>
<p>Genome</p>
<p>Bioarray,</p>
<p>300031</p></td>
<td>GPL2896</td>
<td><p><strong>A-GEHB‑</strong></p>
<p><strong>4</strong></p></td>
<td>GEH</td>
<td>35,129</td>
<td>1</td>
<td>6</td>
<td>6</td>
<td>36</td>
</tr>
<tr class="even">
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td><strong>180</strong></td>
</tr>
</tbody>
</table>

^a^Data from replicating spots were averaged within GeneSpring software
to generate a single value for each unique probe. Therefore, the number
of rows in the normalized data is fewer than that in the original data
files from Agilent's Feature Extraction software. The rat toxicogenomics
data set was analyzed in Guo, L. *et al. Nature Biotechnology,*
**24(9),** 2006.

+---+---+------------+---+------+-----------------------------------------+
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | * |            |   |      |                                         |
|   | * |            |   |      |                                         |
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|   | a |            |   |      |                                         |
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|   | l |            |   |      |                                         |
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|   | 5 |            |   |      |                                         |
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|   |   |            |   |      |                                         |
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|   | t |            |   |      |                                         |
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|   | I |            |   |      |                                         |
|   | I |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | I |            |   |      |                                         |
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|   | c |            |   |      |                                         |
|   | l |            |   |      |                                         |
|   | u |            |   |      |                                         |
|   | d |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | d |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | n |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | h |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | M |            |   |      |                                         |
|   | A |            |   |      |                                         |
|   | Q |            |   |      |                                         |
|   | C |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | S |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | u |            |   |      |                                         |
|   | d |            |   |      |                                         |
|   | y |            |   |      |                                         |
|   | : |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | 4 |            |   |      |                                         |
|   | 2 |            |   |      |                                         |
|   | 6 |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | m |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | c |            |   |      |                                         |
|   | r |            |   |      |                                         |
|   | o |            |   |      |                                         |
|   | a |            |   |      |                                         |
|   | r |            |   |      |                                         |
|   | r |            |   |      |                                         |
|   | a |            |   |      |                                         |
|   | y |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | * |            |   |      |                                         |
|   | * |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
| 1 | M |            |   |      | **160** microarrays (four human         |
| \ | A |            |   |      | platforms; four RNA samples).           |
| . | Q |            |   |      |                                         |
|   | C |            |   |      |                                         |
|   | P |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | l |            |   |      |                                         |
|   | o |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | - |            |   |      |                                         |
|   | I |            |   |      |                                         |
|   | ( |            |   |      |                                         |
|   | R |            |   |      |                                         |
|   | N |            |   |      |                                         |
|   | A |            |   |      |                                         |
|   | S |            |   |      |                                         |
|   | a |            |   |      |                                         |
|   | m |            |   |      |                                         |
|   | p |            |   |      |                                         |
|   | l |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | S |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | l |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | c |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | o |            |   |      |                                         |
|   | n |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | : |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   | > |            | 4 |      |                                         |
|   |   |            | 0 |      |                                         |
|   | A |            |   |      |                                         |
|   | F |            |   |      |                                         |
|   | X |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | ( |            |   |      |                                         |
|   | 2 |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | : |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   | > |            | 6 |      |                                         |
|   |   |            | 0 |      |                                         |
|   | A |            |   |      |                                         |
|   | G |            |   |      |                                         |
|   | L |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | ( |            |   |      |                                         |
|   | 2 |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | : |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   | > |            | 4 |      |                                         |
|   |   |            | 0 |      |                                         |
|   | G |            |   |      |                                         |
|   | E |            |   |      |                                         |
|   | H |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | ( |            |   |      |                                         |
|   | 2 |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | : |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   | > |            | 2 |      |                                         |
|   |   |            | 0 |      |                                         |
|   | I |            |   |      |                                         |
|   | L |            |   |      |                                         |
|   | M |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | ( |            |   |      |                                         |
|   | 1 |            |   |      |                                         |
|   | > |            |   |      |                                         |
|   |   |            |   |      |                                         |
|   | s |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | : |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
| 2 | M |            |   |      | **266** microarrays (six human          |
| \ | A |            |   |      | platforms; 13 titration points).        |
| . | Q |            |   |      |                                         |
|   | C |            |   |      |                                         |
|   | P |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | l |            |   |      |                                         |
|   | o |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | - |            |   |      |                                         |
|   | I |            |   |      |                                         |
|   | I |            |   |      |                                         |
|   | ( |            |   |      |                                         |
|   | R |            |   |      |                                         |
|   | N |            |   |      |                                         |
|   | A |            |   |      |                                         |
|   | S |            |   |      |                                         |
|   | a |            |   |      |                                         |
|   | m |            |   |      |                                         |
|   | p |            |   |      |                                         |
|   | l |            |   |      |                                         |
|   | e |            |   |      |                                         |
|   | T |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | r |            |   |      |                                         |
|   | a |            |   |      |                                         |
|   | t |            |   |      |                                         |
|   | i |            |   |      |                                         |
|   | o |            |   |      |                                         |
|   | n |            |   |      |                                         |
|   | ) |            |   |      |                                         |
|   | : |            |   |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   | AFX (1     | 4 |      |                                         |
|   |   | site):     | 5 |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   | AGL (1     | 4 |      |                                         |
|   |   | site)      | 5 |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   | AG1 (1     | 4 |      |                                         |
|   |   | site):     | 5 |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   | GEH (1     | 4 |      |                                         |
|   |   | site):     | 6 |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   | ILM (1     | 5 |      |                                         |
|   |   | site):     | 1 |      |                                         |
+---+---+------------+---+------+-----------------------------------------+
|   |   | N/A (1     | 3 |      |                                         |
|   |   | site):     | 4 |      |                                         |
+---+---+------------+---+------+-----------------------------------------+

> **Table 6. The total number of microarrays used in the MAQC project:**
> 1,329

+-------------------------------+--------------------------------------+
| > **Category**                | **Number of Microarrays**            |
+-------------------------------+--------------------------------------+
| > Official                    | 573                                  |
+-------------------------------+--------------------------------------+
| > Additional                  | 130                                  |
+-------------------------------+--------------------------------------+
| > Tumor                       | 20                                   |
+-------------------------------+--------------------------------------+
| > Rat Toxicogenomics          | 180                                  |
+-------------------------------+--------------------------------------+
| > Pilots (I and II)           | 426                                  |
+-------------------------------+--------------------------------------+
| > ***Total***                 | ***1,329***                          |
+-------------------------------+--------------------------------------+

> Data from **903** microarrays (Official-573 + Additional-130 +
> Tumor-20 + Rat Toxicogenomics-180) based on 19 platforms need to be
> deposited into GEO and ArrayExpress. In addition, expression data from
> three alternative platforms (TAQ, QGN, and GEX) are also deposited,
> corresponding to **40** "virtual" microarrays in public database
> records (e.g., GEO GSM numbers). In total, there will be **943** GSM
> records in GEO.
>
> *Note: Pilot-I and Pilot-II data (426 microarrays) will not be
> deposited in public repositories until further notice.*
>
> **Table 7. Original MAQC Data Files Distributed under
> [[http://edkb.fda.gov/MAQC/MainStudy/upload/]{.underline}](http://edkb.fda.gov/MAQC/MainStudy/upload/)**

+---+--------------------+---------------------------------------------+
| * | > **Filename**     | > **Description of the Original Data**      |
| * |                    |                                             |
| N |                    |                                             |
| o |                    |                                             |
| . |                    |                                             |
| * |                    |                                             |
| * |                    |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQC             | > ABI non-normalized data.                  |
|   | > \_               |                                             |
|   | ABI_123_60TXTs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 2 | > MAQC_AFX_        | > Affymetrix CEL files.                     |
|   | 123456_120CELs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 3 | > MAQC_            | > Agilent FE8.5 output files.               |
|   | AG1_123_60TXTs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 4 | > MAQC_            | > Agilent FE8.5 output files.               |
|   | AGL_123_60TXTs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 5 | > MAQC             | > Output from SpotData software (CapitalBio |
|   | _BIO1_1_10LSRs.zip | > Corp.).                                   |
+---+--------------------+---------------------------------------------+
| 6 | > MAQ              | > Output from SpotData software (CapitalBio |
|   | C_BIO_1_20LSRs.zip | > Corp.).                                   |
+---+--------------------+---------------------------------------------+
| 7 | > MAQC_EPP_        | > Each array was scanned at three different |
|   | 123_180TXTGPRs.zip | > PMT gain settings.                        |
+---+--------------------+---------------------------------------------+
| 8 | > MAQC_GEH_1       | > GenePix 4000B output files.               |
|   | 232Fail_80TXTs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 9 | > GEX              | > N/A                                       |
+---+--------------------+---------------------------------------------+
| 1 | > MAQC_H2          | > GenePix output files.                     |
| 0 | 5K1_123_30GPRs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQC             | > GenePix output files.                     |
| 1 | _H25K_2_30GPRs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQC_I           | > Illumina non-normalized data.             |
| 2 | >                  |                                             |
|   |  LM_123_59TXTs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQC_NCI         | > GenePix output files.                     |
| 3 | 2nd_3r4_20GPRs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQC_NCI_122Fa   | > GenePix output files.                     |
| 4 | il3Fail_74GPRs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQ              | > GenePix output files.                     |
| 5 | C_NMC_1_10GPRs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQ              | > GenePix output files.                     |
| 6 | C_OPN_1_10GPRs.zip |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > QGN              | > N/A                                       |
| 7 |                    |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > MAQ              | > Original data from ABI, Affymetrix,       |
| 8 | C_Rat_180Files.zip | > Agilent, and GE Healthcare platforms.     |
+---+--------------------+---------------------------------------------+
| 1 | > TAQ              | > N/A                                       |
| 9 |                    |                                             |
+---+--------------------+---------------------------------------------+
| 2 | > MAQ              | > Affymetrix CEL files.                     |
| 0 | C_Tumor_20CELs.zip |                                             |
+---+--------------------+---------------------------------------------+

\*You can download ALL original data in one single file from GEO at
[[ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE5350/]{.underline}](ftps://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE5350/)
(3.99 GB!).

**Table 8. Normalized MAQC Data Files Distributed under
[[http://edkb.fda.gov/MAQC/MainStudy/upload/]{.underline}](http://edkb.fda.gov/MAQC/MainStudy/upload/)**

+---+--------------------+---------------------------------------------+
| * | > **Filename**     | > **Description of the Normalized Data**    |
| * |                    |                                             |
| N |                    |                                             |
| o |                    |                                             |
| . |                    |                                             |
| * |                    |                                             |
| * |                    |                                             |
+---+--------------------+---------------------------------------------+
| 1 | > norm_MAQC        | > The signal value is the fully corrected,  |
|   | > \                | > background subtracted measurement of      |
|   | _ABI_123_qNorm.zip | > chemiluminescent signal for gene          |
|   |                    | >                                           |
|   |                    | > expression values. Data were              |
|   |                    | > quantile-normalized per test site (20     |
|   |                    | > arrays).                                  |
+---+--------------------+---------------------------------------------+
| 2 | > norm_MAQC        | > The CEL file data were analyzed with      |
|   | > \_AFX_1          | > BioConductor to generate probeset level   |
|   | 23456_qPLIER16.zip | > data using the justPlier() function.      |
|   |                    | >                                           |
|   |                    | > Probe-level data were quantile normalized |
|   |                    | > before PLIER summarization per test site  |
|   |                    | > (20 arrays). An offset value of           |
|   |                    | >                                           |
|   |                    | > 16 was then added to each probeset-level  |
|   |                    | > data point.                               |
+---+--------------------+---------------------------------------------+
| 3 | > norm_MAQC \_AG   | > Data were transformed by setting all      |
|   | > 1_123_Median 1   | > measurements less than 5.0 to 5.0. Data   |
|   | > GeneSpring.      | > points that did not have detectable       |
|   | >                  | >                                           |
|   | > zip              | > signal and those that represent           |
|   |                    | > microarray controls were labeled as       |
|   |                    | > Absent, those representing either         |
|   |                    | > non-uniform or                            |
|   |                    | >                                           |
|   |                    | > saturated features were labeled as        |
|   |                    | > Marginal, and all remaining data points   |
|   |                    | > were labeled as Present. All data points  |
|   |                    | >                                           |
|   |                    | > were median-scaled to 1 using the median  |
|   |                    | > signal intensity value for data points    |
|   |                    | > labeled as Present.                       |
+---+--------------------+---------------------------------------------+
| 4 | > norm_MAQC        | > Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3   |
|   | > \                | > and Cy5 channel intensities               |
|   | _AGL_123_FE8.5.zip | > (background-subtracted). Data were        |
|   |                    | >                                           |
|   |                    | > extracted using Agilent\'s Feature        |
|   |                    | > Extraction software, version 8.5 (P/N     |
|   |                    | > G2567AA). AGL sample-pair convention:     |
|   |                    | >                                           |
|   |                    | > A (A/A, Cy3/Cy5), B (B/B, Cy3/Cy5), C     |
|   |                    | > (A/B, Cy3/Cy5), and D (B/A, Cy3/Cy5).     |
|   |                    | > Only MAQC samples A and B                 |
|   |                    | >                                           |
|   |                    | > were used in AGL two-color experiments.   |
+---+--------------------+---------------------------------------------+
| 5 | > norm_MAQC_BIO    | > Slides were scanned with a confocal       |
|   | 1_1_Median1000.zip | > LuxScan scanner (CapitalBio Corp.). The   |
|   |                    | > data from the obtained images were        |
|   |                    | >                                           |
|   |                    | > extracted with SpotData software          |
|   |                    | > (CapitalBio Corp.). Median-scaling of     |
|   |                    | > background-subtracted intensity was       |
|   |                    | >                                           |
|   |                    | > applied to each array to make median      |
|   |                    | > equal to 1000.                            |
+---+--------------------+---------------------------------------------+
| 6 | >                  | > Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3   |
|   | norm_MAQC_BIO_1_Me | > and Cy5 channel intensities               |
|   | dian1000Lowess.zip | > (background-subtracted). The data from    |
|   |                    | > the                                       |
|   |                    | >                                           |
|   |                    | > obtained images were extracted with       |
|   |                    | > SpotData software (CapitalBio Corp.). The |
|   |                    | > raw data were submitted to MAQC           |
|   |                    | >                                           |
|   |                    | > and further normalized by using           |
|   |                    | > linear-scaling (to median of 1000) and    |
|   |                    | > LOWESS. BIO sample-pair convention: A     |
|   |                    | >                                           |
|   |                    | > (A/B, Cy3/Cy5), B (B/A, Cy3/Cy5), sA      |
|   |                    | > (A/A, Cy3/Cy5), sB (B/B, Cy3/Cy5). The    |
|   |                    | > human genome-wide long                    |
|   |                    | >                                           |
|   |                    | > oligonucleotide microarray was            |
|   |                    | > constructed inhouse at CapitalBio         |
|   |                    | > Corporation, Beijing, China.              |
+---+--------------------+---------------------------------------------+
| 7 | > norm_MAQC        | > Each array was scanned at three different |
|   | _EPP_123_Ratio.zip | > PMT gain settings. Eppendorf has          |
|   |                    | > developed specialized data analysis       |
|   |                    | >                                           |
|   |                    | > scheme treating the scanning, the         |
|   |                    | > background correction and normalization   |
|   |                    | > in a suited framework for low density     |
|   |                    | >                                           |
|   |                    | > arrays generating array to array gene     |
|   |                    | > expression ratio. The data sets submitted |
|   |                    | > are divided in two groups. The first      |
|   |                    | >                                           |
|   |                    | > data set (norm) provides gene expression  |
|   |                    | > ratio comparing two samples and           |
|   |                    | > constitutes the standard result for the   |
|   |                    | >                                           |
|   |                    | > Eppendorf platform. Provided here are     |
|   |                    | > ratio data (compared to sample A1 for     |
|   |                    | > each test site).                          |
+---+--------------------+---------------------------------------------+
| 8 | > norm_MAQC_GEH_12 | > Local background subtracted intensity     |
|   | 32Fail_Median1.zip | > data after median-scaling each array to a |
|   |                    | > median of 1. GEH\'s original flag         |
|   |                    | >                                           |
|   |                    | > information (\'Quality_flag\') is         |
|   |                    | > provided: G = \'Good\', L = \'Absent\', S |
|   |                    | > = \'Saturated\', M = \'Manufacturing      |
|   |                    | > Defect\', I =                             |
|   |                    | >                                           |
|   |                    | > \'Irregular Shape\', C = \'Contaminated   |
|   |                    | > Spot\'.                                   |
+---+--------------------+---------------------------------------------+
| 9 | > norm_MAQC_GEX    | > The data values are the number of         |
|   | > \_1 \_ACTB.zip   | > molecules normalized to 1,000,000 ACTB    |
|   |                    | > molecules. No threshold was set;          |
|   |                    | >                                           |
|   |                    | > every gene was identified as Present      |
|   |                    | > (\"0\").                                  |
+---+--------------------+---------------------------------------------+
| 1 | > norm_MAQC_H25K1_ | > Local background subtracted intensity     |
| 0 | 123_Median1000.zip | > data after median-scaling each array to a |
|   |                    | > median of 1,000. GenePix\'s original      |
|   |                    | >                                           |
|   |                    | > flagging information - 0: Good; -50: Not  |
|   |                    | > found; -75: Absent; -100: Bad             |
+---+--------------------+---------------------------------------------+
| 1 | > norm_            | > Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3   |
| 1 | MAQC_H25K_2_Median | > and Cy5 channel intensities               |
|   | > 1000Lowess.zi    | > (background-subtracted). The raw data     |
|   | >                  | >                                           |
|   | > p                | > were submitted to MAQC and further        |
|   |                    | > normalized by using linear-scaling (to    |
|   |                    | > median of 1000) and LOWESS. H25K          |
|   |                    | >                                           |
|   |                    | > two-color sample-pair convention: A (A/B, |
|   |                    | > Cy3/Cy5), B (B/A, Cy3/Cy5), sA (A/A,      |
|   |                    | > Cy3/Cy5), and sB (B/B,                    |
|   |                    | >                                           |
|   |                    | > Cy3/Cy5). Only test site 2 submitted      |
|   |                    | > two-color H25K data.                      |
+---+--------------------+---------------------------------------------+
| 1 | > norm_MAQC_I      | > Data was processed using Illumina         |
| 2 | LM_123_qNorm16.zip | > BeadStudio version 1.5.0.34 software      |
|   |                    | > using background subtraction and cubic    |
|   |                    | >                                           |
|   |                    | > spline normalization using quantile (20   |
|   |                    | > arrays per test site). Normalized         |
|   |                    | > hybridization intensity values were       |
|   |                    | >                                           |
|   |                    | > adjusted by adding a constant such that   |
|   |                    | > the lowest intensity value for any sample |
|   |                    | > equaled 16. Flag_Detection =              |
|   |                    | >                                           |
|   |                    | > Present: \>= 0.99, Absent: \<0.99.        |
+---+--------------------+---------------------------------------------+

+---+--------------------+---------------------------------------------+
| 1 | > norm \_MAQC_NCI2 | > Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3   |
| 3 | > \_3r4 \_Median   | > and Cy5 channel intensities               |
|   | > 1000Lowess.      | > (background-subtracted). The raw data     |
|   | >                  | >                                           |
|   | > zip              | > were submitted to MAQC and further        |
|   |                    | > normalized by using linear-scaling (to    |
|   |                    | > median of 1000) and LOWESS. NCI2          |
|   |                    | >                                           |
|   |                    | > sample-pair convention: A (A/B, Cy3/Cy5), |
|   |                    | > B (B/A, Cy3/Cy5), sA (A/A, Cy3/Cy5). This |
|   |                    | > is the second (and                        |
|   |                    | >                                           |
|   |                    | > different) printing of the NCI.           |
|   |                    | > GenePix\'s original flagging              |
|   |                    | > information, - 0: Good; -50: Not found;   |
|   |                    | > -75: Absent; -                            |
|   |                    | >                                           |
|   |                    | > 100: Bad                                  |
+---+--------------------+---------------------------------------------+
| 1 | > no               | > Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3   |
| 4 | rm_MAQC_NCI_122Fai | > and Cy5 channel intensities               |
|   | l3Fail_Median1000L | > (background-subtracted). The raw data     |
|   | >                  | >                                           |
|   | > owess.zi p       | > were submitted to MAQC and further        |
|   |                    | > normalized by using linear-scaling (to    |
|   |                    | > median of 1000) and LOWESS. NCI           |
|   |                    | >                                           |
|   |                    | > sample-pair convention: A (A/A, Cy3/Cy5), |
|   |                    | > B (B/A, Cy3/Cy5), C (C/A, Cy3/Cy5), and D |
|   |                    | > (D/A, Cy3/Cy5). MAQC                      |
|   |                    | >                                           |
|   |                    | > sample A was used as the common reference |
|   |                    | > sample (Cy5; channel 2) in NCI two-color  |
|   |                    | > experiments. Test sites                   |
|   |                    | >                                           |
|   |                    | > NCI_2 and NCI_3 failed in the first round |
|   |                    | > of experiments due to protocol issues.    |
|   |                    | > The failed hybridizations are             |
|   |                    | >                                           |
|   |                    | > named as NCI_2Fail and NCI_3Fail. NCI \_2 |
|   |                    | > repeated part of the experiment with 14   |
|   |                    | > hybridizations. Site NCI_3                |
|   |                    | >                                           |
|   |                    | > repeated part of the experiment with the  |
|   |                    | > 2^nd^ NCI printing (NCI_3r). GenePix\'s   |
|   |                    | > original flagging information, - 0:       |
|   |                    | >                                           |
|   |                    | > Good; -50: Not found; -75: Absent; -100:  |
|   |                    | > Bad                                       |
+---+--------------------+---------------------------------------------+
| 1 | >                  | > Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3   |
| 5 | norm_MAQC_NMC_1_Me | > and Cy5 channel intensities               |
|   | dian1000Lowess.zip | > (background-subtracted). Images were      |
|   |                    | >                                           |
|   |                    | > processed and quantified using GenePix    |
|   |                    | > Pro 6.0.0.56. The data were filtered (or  |
|   |                    | > flagged) on the basis of signal levels    |
|   |                    | >                                           |
|   |                    | > and spot quality. The raw data were       |
|   |                    | > submitted to MAQC and further normalized  |
|   |                    | > by using linear median-scaling (to        |
|   |                    | >                                           |
|   |                    | > median of 1000) and LOWESS. NMC           |
|   |                    | > sample-pair convention: A (A/B, Cy3/Cy5), |
|   |                    | > B (B/A, Cy3/Cy5). The slides              |
|   |                    | >                                           |
|   |                    | > were printed by the Norwegian Microarray  |
|   |                    | > Consortium. GenePix\'s original flagging  |
|   |                    | > information, - 0: Good; -50:              |
|   |                    | >                                           |
|   |                    | > Not found; -75: Absent; -100: Bad         |
+---+--------------------+---------------------------------------------+
| 1 | >                  | > Images were processed and quantified      |
| 6 | norm_MAQC_OPN_1_Me | > using GenePix Pro. The data were filtered |
|   | dian1000Lowess.zip | > (or flagged) on the basis of signal       |
|   |                    | >                                           |
|   |                    | > levels and spot quality. The raw data     |
|   |                    | > were submitted to MAQC and further        |
|   |                    | > normalized by using linear median‑        |
|   |                    | >                                           |
|   |                    | > scaling (to median of 1000) and LOWESS.   |
|   |                    | > GenePix\'s original flagging              |
|   |                    | > information, - 0: Good; -50: Not found;   |
|   |                    | > -75:                                      |
|   |                    | >                                           |
|   |                    | > Absent; -100: Bad                         |
+---+--------------------+---------------------------------------------+
| 1 | > norm_MAQ         | > Background signals were determined in the |
| 7 | C_QGN_1_Signal.zip | > absence of RNA samples and subtracted     |
|   |                    | > from signals obtained in the              |
|   |                    | >                                           |
|   |                    | > presence of RNA samples. Because          |
|   |                    | > QuantiGene assay measures RNA directly,   |
|   |                    | > no data normalization against a           |
|   |                    | >                                           |
|   |                    | > reference gene is required in the data    |
|   |                    | > analysis. Flag_Detection = \"A\": VALUE   |
|   |                    | > \< LOD; \"P\": VALUE \>= LOD.             |
|   |                    | >                                           |
|   |                    | > LOD = limit of detection of the assay,    |
|   |                    | > and equals to \"Background + 3 SD of      |
|   |                    | > Background\".                             |
+---+--------------------+---------------------------------------------+
| 1 | > norm_MAQC_RatTGx | > Each of the five labs ran 36 samples,     |
| 8 | > \_4              | > resulting in 180 microarrays from four    |
|   | Platforms5Labs.zip | > platforms. The data from each lab were    |
|   |                    | >                                           |
|   |                    | > analyzed according to the platform        |
|   |                    | > provider's preferred procedures as        |
|   |                    | > defined above for the human platforms.    |
+---+--------------------+---------------------------------------------+
| 1 | > norm_MAQ         | > POLR2A was chosen as the reference gene   |
| 9 | C_TAQ_1_POLR2A.zip | > and each replicate CT was subtracted from |
|   |                    | > the average POLR2A CT to                  |
|   |                    | >                                           |
|   |                    | > give the log2 difference (delta CT), the  |
|   |                    | > normalized value. For delta CT            |
|   |                    | > calculations, a CT value of 35 was used   |
|   |                    | > for                                       |
|   |                    | >                                           |
|   |                    | > any replicate that had CT \> 35. Provided |
|   |                    | > is the normalized expression value, i.e., |
|   |                    | > CT of POLR2A minus CT of the              |
|   |                    | >                                           |
|   |                    | > tested gene. Thus, a larger value         |
|   |                    | > indicates a higher gene expression level. |
|   |                    | > Flag_Detection = \"A\": CT\>35;           |
|   |                    | >                                           |
|   |                    | > \"P\": CT\<=35.                           |
+---+--------------------+---------------------------------------------+
| 2 | >                  | > The CEL file data were analyzed with      |
| 0 |  norm_MAQC_Tumor_A | > BioConductor to generate probeset level   |
|   | FX_12_qPLIER16.zip | > data using the justPlier() function.      |
|   |                    | >                                           |
|   |                    | > Probe-level data were quantile normalized |
|   |                    | > before PLIER summarization per test site  |
|   |                    | > (10 arrays). An offset value of           |
|   |                    | >                                           |
|   |                    | > 16 was then added to each probeset-level  |
|   |                    | > data point. BioConductor-calculated PLIER |
|   |                    | > Signal intensity with the                 |
|   |                    | >                                           |
|   |                    | > addition of an offset value of 16. Flag   |
|   |                    | > information was generated using           |
|   |                    | > mas5calls() function in BioConductor: P = |
|   |                    | >                                           |
|   |                    | > Present, A = Absent, and M = Marginal.    |
+---+--------------------+---------------------------------------------+

> \*Notes: 1. For quantile normalization, data from each test site were
> considered independently; 2. Detailed array annotation information can
> be found at GEO.
>
> **A list of the 943 GEO GSM records ("microarrays") and the
> corresponding original data files is available at
> [[http://edkb.fda.gov/MAQC/MainStudy/upload/GSE5350_943GSMs_MAQC_FileName_Mapping.txt.]{.underline}](http://edkb.fda.gov/MAQC/MainStudy/upload/GSE5350_943GSMs_MAQC_FileName_Mapping.txt.)**