![](media/image1.jpeg){width="1.0791666666666666in"
height="0.26458333333333334in"}Summary of the MAQC **September-22-2005**
Teleconference

**The MAQC Project: Calibrated RNA Samples, Reference Datasets, and**

**QC Metrics/Thresholds for Microarray Quality Control**

Teleconference Date: September 22, 2005 (9am PDT/11am CDT/12pm EDT/16:00
GMT)

Summary Date: September 26, 2005

Author: Leming Shi, FDA/NCTR, +1-870-543-7387,
[Leming.Shi@fda.hhs.gov](mailto:jfuscoe@nctr.fda.gov)

MAQC URL: <http://edkb.fda.gov/MAQC/>

1.  **RNA Sample Processing**: Each platform provider updated the status
    of RNA sample processing at its test sites. All platform providers
    expressed confidence in meeting the data submission deadline --
    September 30, 2005. The test site and its platform provider should
    contact <Leming.Shi@fda.hhs.gov> if there is any difficulty in
    meeting the deadline.

2.  **MAQC Guidance to Data Analysis**: A draft document on *MAQC
    Guidance to Data Analysis* (v2) that serves as the 5^th^ Appendix of
    the *Main Study Guidance* was distributed to the whole MAQC group on
    September 21 and everyone was invited to comment on the document.
    Each platform provider was given an opportunity to provide its
    preferred procedures for preprocessing and normalizing data
    generated with its platform. Whenever possible, the datasets to be
    distributed to test sites and analysis sites for independent
    analyses will be processed according to manufacturer's preferred
    procedures along with the original, non-normalized intensity values
    (Complete data submission should also include image files that will
    be made available upon request). All the MAQC data will be handled
    within ArrayTrack
    (<http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/>).
    It was emphasized during the TC that criteria should be agreed upon
    for defining subset(s) of genes for cross-platform comparison.
    Specifically, decisions need to be made in handling different
    probe-target (transcript) relationships. Hence, a teleconference has
    been scheduled on Sept 27 for platform providers and data analysis
    sites to discuss probe-transcript mapping. Other interested parties
    should contact <Leming.Shi@fda.hhs.gov> for dial-in information.

3.  **December 1-2, 2005 Meeting**: The next face-to-face MAQC project
    meeting will be held at Crowne Plaza Cabana, Portofino Room
    (December 1, 2005, 8 a.m. -- 5 p.m.) and St. Tropez Room (December
    2, 2005, 8 a.m. -- 2 p.m.), 4290 El Camino Real, Palo Alto,
    CA 94306. Telephone: 650-857-0787; FAX: 650-496-1939; Website:
    <http://www.cppaloalto.crowneplaza.com/>. There will be no
    registration fee for attending the meeting. However, interested
    parties should contact Leming Shi (Telephone: 870-543-7387; FAX:
    870-543-7686; e-mail:
    [leming.shi@fda.hhs.gov](mailto:lshi@nctr.fda.gov)) as soon as
    possible to confirm their participation since the number of
    attendees that can be accommodated will be limited. The focus of the
    meeting will be to review the datasets generated by the MAQC study
    and to discuss the plan for peer-reviewed publication of
    manuscripts.

4.  **Scoreboard**: As of September 25, FDA/NCTR has received datasets
    from eight test sites (congratulations and thanks):

> AFX_1 (Affymetrix, Chunmei Liu) AFX_2 (FDA/CDER, Karol Thompson)
>
> AFX_3 (Ambion, Mike Wilson) AFX_6 (UCLA, Charles Wang)
>
> AGL_2 (FDA/NCTR, Tucker Paterson) AGL_3 (Icoria, Ed Lobenhofer)
>
> ABI_1 (Applied Biosystems, Lu Zhang) ABI_2 (EPA, Mitch Rosen/David
> Dix)

**The next MAQC Teleconference:**

Thursday, October 6, 2005 (9 am PDT / 11 am CDT / 12 pm EDT / 16:00 GMT)

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