> **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>; <http://edkb.fda.gov/MAQC/>;
<http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/>

October 2, 2006, 10:18 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/>.

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

    -   GEO (series accession number: **GSE5350**); All original files
        (e.g. CEL files) can be downloaded as a single tar file at
        <ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE5350/>
        (3.99 GB).

    -   ArrayExpress (accession number: **E-TABM-132**, pending);

    -   ArrayTrack
        (<http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/>);
        and

    -   The MAQC website (<http://edkb.fda.gov/MAQC/MainStudy/upload/>)
        -- a good place to download normalized data (filenames staring
        with "norm\_") in a multi-column table format per platform (see
        Table 8 of this document). The filenames should be
        self-explanatory.

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/>).

5.  Corrections, questions, and comments should be addressed to
    <Leming.Shi@fda.hhs.gov>.

> The total number of microarrays used in the MAQC project:
> **[1,329]{.mark}**

**Table 1. "*Official*" Platforms and Data Included in the MAQC Main
Study: [[573]{.underline}]{.mark} 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><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><strong>Number of Probes</strong></td>
<td><strong>Number of Test Sites</strong></td>
<td><strong>Number of Samples</strong></td>
<td><strong>Number of Replicates</strong></td>
<td><strong>Total Number of Microarrays</strong></td>
</tr>
<tr class="even">
<td>Applied Biosystems</td>
<td>ABI</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td>Human Genome Survey Microarray v2.0</td>
<td>GPL2986</td>
<td><strong>A-MEXP-503</strong></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>5</td>
<td>60</td>
</tr>
<tr class="odd">
<td>Affymetrix</td>
<td>AFX</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td>HG-U133 Plus 2.0 GeneChip®</td>
<td>GPL570</td>
<td><strong>A-AFFY-44</strong></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>5</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">Whole Human Genome Oligo Microarray, G4112A</td>
<td rowspan="2">GPL1708</td>
<td rowspan="2"><strong>A-AGIL-11</strong></td>
<td><p>AGL_1</p>
<p>AGL_2</p>
<p>AGL_3</p></td>
<td rowspan="2"><p>43,931</p>
<p>(same printing; 41058 – GeneSpring<sup>d</sup>)</p></td>
<td>3</td>
<td>2</td>
<td>10</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>5</td>
<td>60</td>
</tr>
<tr class="even">
<td>Eppendorf</td>
<td>EPP</td>
<td>One-Color Microarray</td>
<td>DualChip® Microarray</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>5</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>CodeLink™ Human Whole Genome</td>
<td>GPL2895</td>
<td><strong>A-GEHB-1</strong></td>
<td><p>GEH_1</p>
<p>GEH_2</p>
<p>GEH_3</p>
<p>GEH_2Fail</p></td>
<td>54,359</td>
<td>3<sup>a</sup></td>
<td>4</td>
<td>5</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 BeadChip,</p>
<p>48K v1.0</p></td>
<td>GPL2507</td>
<td><strong>A-MEXP-524</strong></td>
<td><p>ILM_1</p>
<p>ILM_2</p>
<p>ILM_3</p></td>
<td>47,293</td>
<td>3<sup>b</sup></td>
<td>4</td>
<td>5</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>Operon Human Oligo Set v3</td>
<td>GPL4108</td>
<td><strong>A-MEXP-573</strong></td>
<td><p>NCI_1</p>
<p>NCI_2</p>
<p>NCI_2Fail</p>
<p>NCI_3Fail</p></td>
<td>37,632</td>
<td>3<sup>c</sup></td>
<td>4</td>
<td>5</td>
<td>74</td>
</tr>
<tr class="even">
<td><em>Applied Biosystems</em></td>
<td><em>TAQ</em></td>
<td><em>TaqMan® Assays</em></td>
<td><em>&gt;200,000 assays available</em></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><em>4</em></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><em>~2,600 assays available</em></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><em>3</em></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™</em></p>
<p><em>Assays</em></p></td>
<td><em>~1,000 assays available</em></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><em>3</em></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]{.mark} "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]{.underline}]{.mark} 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: 7%" />
<col style="width: 7%" />
<col style="width: 18%" />
<col style="width: 7%" />
<col style="width: 9%" />
<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><strong>Number of Probes</strong></td>
<td><strong>Test Sites</strong></td>
<td><strong>Number of Samples</strong></td>
<td><strong>Number of Replicates</strong></td>
<td><p><strong>Number of Microarrays</strong></p>
<p><strong>Per Test Site</strong></p></td>
</tr>
<tr class="even">
<td rowspan="2">NCI_Operon (2<sup>nd</sup> printing)</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>NCI_4: Harvard University</td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="odd">
<td>NCI_3r: FDA/CBER (repeat)</td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td rowspan="2">CapitalBio_ Operon</td>
<td>BIO</td>
<td><p>Two-Color</p>
<p>Microarray</p></td>
<td rowspan="2">GPL4187</td>
<td rowspan="2"><strong>A-MEXP-576</strong></td>
<td>BIO_1</td>
<td rowspan="2"><p>23,232</p>
<p>(same printing)</p></td>
<td>BIO_1: CapitalBio</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>BIO1_1</td>
<td>BIO1_1: CapitalBio</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><strong>A-MEXP-574</strong></td>
<td>OPN_1</td>
<td>37,584</td>
<td>OPN_1: Operon</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><strong>A-MEXP-552</strong></td>
<td>NMC_1</td>
<td>36,288</td>
<td>NMC_1: Norwegian Microarray Consortium</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 rowspan="4"><strong>A-MEXP-575</strong></td>
<td>H25K_2</td>
<td rowspan="4"><p>27,648</p>
<p>(same printing)</p></td>
<td>H25K_2: Yale University</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"><p>H25K1_1</p>
<p>H25K1_2</p>
<p>H25K1_3</p></td>
<td>H25K1_1: TeleChem</td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="even">
<td>H25K1_2: Yale University</td>
<td>2</td>
<td>5</td>
<td>10</td>
</tr>
<tr class="odd">
<td>H25K1_3: Wake Forest University</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]{.underline}]{.mark} 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><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><strong>Number of Probes</strong></td>
<td><strong>Number of Test Sites</strong></td>
<td><strong>Number of Samples</strong></td>
<td><strong>Number of Replicates</strong></td>
<td><strong>Total Number of Microarrays</strong></td>
</tr>
<tr class="even">
<td>Affymetrix</td>
<td>AFX</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td>HG-U133 Plus 2.0 GeneChip®</td>
<td>GPL570</td>
<td><strong>A-AFFY-44</strong></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]{.mark} 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><strong>Number of Probes</strong></td>
<td><strong>Number of Test Sites</strong></td>
<td><strong>Number of Samples</strong></td>
<td><strong>Number of Replicates</strong></td>
<td><strong>Total Number of Microarrays</strong></td>
</tr>
<tr class="even">
<td>Applied Biosystems</td>
<td>ABI</td>
<td><p>One-Color</p>
<p>Microarray</p></td>
<td><p>Rat Genome</p>
<p>Survey Microarray</p></td>
<td>GPL2996</td>
<td><strong>A-MEXP-565</strong></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>Rat Genome 230 2.0 GeneChip®</td>
<td>GPL1355</td>
<td><strong>A-AFFY-43</strong></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>Microarray</p></td>
<td><p>Whole</p>
<p>Rat Genome Oligo Microarray, G4131A</p></td>
<td>GPL2877</td>
<td><strong>A-AGIL-19</strong></td>
<td>AG1</td>
<td><p>43,628</p>
<p>(41,070 – 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>Rat Whole Genome Bioarray, 300031</td>
<td>GPL2896</td>
<td><strong>A-GEHB-4</strong></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.

**Table 5. "*Pilots*" Data (Pilot-I and Pilot-II) Included in the MAQC
Study: [[426]{.underline}]{.mark} microarrays**

1.  MAQC Pilot-I (RNA Sample Selection): **160** microarrays (four human
    platforms; four RNA samples).

> AFX (2 sites): 40
>
> AGL (2 sites): 60
>
> GEH (2 sites): 40
>
> ILM (1 site): 20

2.  MAQC Pilot-II (RNA Sample Titration): **266** microarrays (six human
    platforms; 13 titration points).

> AFX (1 site): 45
>
> AGL (1 site) 45
>
> AG1 (1 site): 45
>
> GEH (1 site): 46
>
> ILM (1 site): 51
>
> N/A (1 site): 34
>
> **Table 6. The total number of microarrays used in the MAQC project:
> [1,329]{.mark}**

  -------------------------------- --------------------------------------
  **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/>**

  --------- ---------------------------------- ---------------------------------------------
  **No.**   **Filename**                       **Description of the Original Data**

  1         MAQC_ABI_123_60TXTs.zip            ABI non-normalized data.

  2         MAQC_AFX_123456_120CELs.zip        Affymetrix CEL files.

  3         MAQC_AG1_123_60TXTs.zip            Agilent FE8.5 output files.

  4         MAQC_AGL_123_60TXTs.zip            Agilent FE8.5 output files.

  5         MAQC_BIO1_1_10LSRs.zip             Output from SpotData software (CapitalBio
                                               Corp.).

  6         MAQC_BIO_1_20LSRs.zip              Output from SpotData software (CapitalBio
                                               Corp.).

  7         MAQC_EPP_123_180TXTGPRs.zip        Each array was scanned at three different PMT
                                               gain settings.

  8         MAQC_GEH_1232Fail_80TXTs.zip       GenePix 4000B output files.

  9         GEX                                N/A

  10        MAQC_H25K1_123_30GPRs.zip          GenePix output files.

  11        MAQC_H25K_2_30GPRs.zip             GenePix output files.

  12        MAQC_ILM_123_59TXTs.zip            Illumina non-normalized data.

  13        MAQC_NCI2nd_3r4_20GPRs.zip         GenePix output files.

  14        MAQC_NCI_122Fail3Fail_74GPRs.zip   GenePix output files.

  15        MAQC_NMC_1_10GPRs.zip              GenePix output files.

  16        MAQC_OPN_1_10GPRs.zip              GenePix output files.

  17        QGN                                N/A

  18        MAQC_Rat_180Files.zip              Original data from ABI, Affymetrix, Agilent,
                                               and GE Healthcare platforms.

  19        TAQ                                N/A

  20        MAQC_Tumor_20CELs.zip              Affymetrix CEL files.
  --------- ---------------------------------- ---------------------------------------------

\*You can download ALL original data in one single file from GEO at
<ftp://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/>**

  --------- ------------------------------------------------- ----------------------------------------------
  **No.**   **Filename**                                      **Description of the Normalized Data**

  1         norm_MAQC_ABI_123_qNorm.zip                       The signal value is the fully corrected,
                                                              background subtracted measurement of
                                                              chemiluminescent signal for gene expression
                                                              values. Data were quantile-normalized per test
                                                              site (20 arrays).

  2         norm_MAQC_AFX_123456_qPLIER16.zip                 The CEL file data were analyzed with
                                                              BioConductor to generate probeset level 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_AG1_123_Median1GeneSpring.zip           Data were transformed by setting all
                                                              measurements less than 5.0 to 5.0. Data points
                                                              that did not have detectable 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_AGL_123_FE8.5.zip                       Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3 and
                                                              Cy5 channel intensities
                                                              (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_BIO1_1_Median1000.zip                   Slides were scanned with a confocal 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         norm_MAQC_BIO_1_Median1000Lowess.zip              Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3 and
                                                              Cy5 channel intensities
                                                              (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_EPP_123_Ratio.zip                       Each array was scanned at three different 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_1232Fail_Median1.zip                Local background subtracted intensity 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_1_ACTB.zip                          The data values are the number of molecules
                                                              normalized to 1,000,000 ACTB molecules. No
                                                              threshold was set; every gene was identified
                                                              as Present (\"0\").

  10        norm_MAQC_H25K1_123_Median1000.zip                Local background subtracted intensity 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

  11        norm_MAQC_H25K_2_Median1000Lowess.zip             Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3 and
                                                              Cy5 channel intensities
                                                              (background-subtracted). The raw data 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.

  12        norm_MAQC_ILM_123_qNorm16.zip                     Data was processed using Illumina 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.

  13        norm_MAQC_NCI2_3r4_Median1000Lowess.zip           Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3 and
                                                              Cy5 channel intensities
                                                              (background-subtracted). The raw data 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

  14        norm_MAQC_NCI_122Fail3Fail_Median1000Lowess.zip   Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3 and
                                                              Cy5 channel intensities
                                                              (background-subtracted). The raw data 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 wit hthe 2^nd^
                                                              NCI printing (NCI_3r). GenePix\'s original
                                                              flagging information, - 0: Good; -50: Not
                                                              found; -75: Absent; -100: Bad

  15        norm_MAQC_NMC_1_Median1000Lowess.zip              Ratio defined as CH1/CH2 (Cy3/Cy5), Cy3 and
                                                              Cy5 channel intensities
                                                              (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

  16        norm_MAQC_OPN_1_Median1000Lowess.zip              Images were processed and quantified using
                                                              GenePix Pro. 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.
                                                              GenePix\'s original flagging information, - 0:
                                                              Good; -50: Not found; -75: Absent; -100: Bad

  17        norm_MAQC_QGN_1_Signal.zip                        Background signals were determined in the
                                                              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 + 3SD of Background\".

  18        norm_MAQC_RatTGx_4Platforms5Labs.zip              Each of the five labs ran 36 samples,
                                                              resulting in 180 microarrays from four
                                                              platforms. The data from each lab were
                                                              analyzed according to the platform provider's
                                                              preferred procedures as defined above for the
                                                              human platforms.

  19        norm_MAQC_TAQ_1_POLR2A.zip                        POLR2A was chosen as the reference gene 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.

  20        norm_MAQC_Tumor_AFX_12_qPLIER16.zip               The CEL file data were analyzed with
                                                              BioConductor to generate probeset level 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>.**