![](media/image1.jpeg){width="1.0791666666666666in"
height="0.26458333333333334in"}Summary of the MAQC **November-17-2005**
Teleconference

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

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

Teleconference Date: November 17, 2005 (9 am PST/11 am CST/12 pm
EST/17:00 GMT)

Summary Date: November 21, 2005

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

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

1.  **Update on Data** **Access** (Leming Shi): An e-mail message on the
    confidentiality conditions for accessing and analyzing the MAQC
    datasets was sent to 38 organizations (27 test sites, 10 data
    analysis sites, and Stratagene) on Oct-24-2005. As of Nov-16-2005,
    22 organizations have agreed to the "conditions" and have been given
    instructions for downloading the datasets. Twenty-one of the 22
    organizations (including 8 of the 10 analysis sites and 9 of the 10
    platform providers) called Leming Shi to obtain the password.

2.  **Initial Data** **Analysis** **and General Conclusions/Concerns**:
    Rick Jensen and a few others raised concerns about the EPP and NCI
    datasets and encouraged both platform providers to take a closer
    look at their datasets. Leming Shi explained that the normalized EPP
    data should be considered as "log ratios" in which one of the
    replicates from sample A was used as the reference. The value of
    keeping the datasets in the study has been emphasized.

3.  **Agilent's One-color Data Generation/Submission** (Jim Collins):
    The three test sites are expected to submit one-color data to
    FDA/NCTR by Nov-23-2005. Pilot Titration data (45 arrays) will also
    be submitted according to the same timeline. Jim Collins stated
    Agilent's desire of treating the one-color data as its primary
    dataset for the MAQC study so that the experimental design would be
    exactly the same as other one-color platforms and the data analysis
    would be greatly simplified. The MAQC group agreed to Agilent's
    request and was happy to see data on samples C and D in the
    one-color design. FDA/NCTR will distribute the one-color data to
    analysis sites as soon as possible. Official data analysis sites
    agreed to analyze the one-color data before the December
    face-to-face meeting. The one-color data will be named as the
    "***AG1***" platform.

4.  **TeleChem ArrayIt** (Leming Shi): TeleChem ArrayIt has been
    planning to generate data following the MAQC guidance with its H25K
    Human Genome Microarrays
    (<http://arrayit.com/Products/Microarrays/H25K/h25k.html>). RNA
    samples A and B were purchased from Stratagene and Ambion,
    respectively, and mixed at TeleChem ArrayIt to produce mixtures C
    and D. RNA samples are being distributed to three test sites. Dr.
    Mark Schena has been invited to give a brief presentation at the
    face-to-face meeting when the MAQC group will decide if the H25K
    arrays should be included in the main study as an additional
    platform.

5.  **December Meeting Agenda** (Leming Shi):

-   The tentative Agenda was reviewed. Everyone was invited to make
    suggestions.

-   It has been emphasized that the results to be presented at the
    meeting should be considered preliminary and for the purpose of
    stimulating discussions regarding future directions of data
    analyses.

-   Ninety people have registered for the MAQC meeting as of
    Nov-16-2005.

-   Speakers: Provide a brief title of your presentation if you have not
    done so.

-   Chairs/panelists: Contact Leming if you are not available for the
    scheduled time.

-   Registered participants: Contact Leming if you changed your mind.

-   If you or your colleagues have not yet registered but plan to attend
    the meeting, you should contact <Leming.Shi@fda.hhs.gov> to secure
    your space at the meeting.

-   Conference call will be set up and the entire meeting (presentations
    and discussion sessions) will be recorded. However, concerns were
    raised regarding the potential disruption by teleconference calls.

-   PPT slides: Concerns were raised to concurrently display PowerPoint
    slides at Affymetrix's Microarray Bulletin website. The main
    concerns were the preliminary nature of the results to be presented
    and the appearance of bias to have the slides displayed at a website
    run by one of the major participating platform providers. It was
    decided not to make PPT slides viewable from the Affymetrix
    Microarray Bulleting website. However, speakers agreed to provide
    slides to teleconference participants from the FDA headquarters.

-   Participants are welcome to distribute materials (*e.g*., reprints,
    PPT slides) related to the theme of the MAQC meeting.

6.  **Promoting the MAQC Effort** (Leming Shi, Rick Jensen, Damir
    Herman, and Jean Thierry‑Mieg)

-   A panel discussion about the MAQC project at the CHI Quantitative
    PCR meeting, San Diego, CA has been scheduled on March 20, 2006.
    Panelists: Shawn Baker, Kathy Lee, Yuling Luo, Leming Shi, Jim
    Willey, and Paul Wolber. Leming Shi explained that they represented
    three alternative platform providers (Kathy, Yuling, and Jim), Shawn
    (located in San Diego), and Paul (is scheduled to give a
    presentation prior to the panel discussion).

-   Affymetrix Microarray Bulletin will post a news item about the MAQC
    project based on a telephone interview with Rick Jensen and Leming
    Shi. News items by other organizations are welcome and will be
    accommodated.

-   Jean Thierry-Mieg (NCBI) briefly mentioned the MAQC project in his
    presentation at "*Transcriptome 2005: From Functional Genomics to
    Systems Biology*", Nov 8, 2005, Shanghai, China.

-   Damir Herman (NCBI) was asked to give a presentation at a microarray
    user group at the NIH on December 8, 2005 to present the general
    aspects of the MAQC project and the sequence-mapping work that Damir
    has been doing.

**Location of the MAQC December Meeting**:

The meeting will be held on December 1-2, 2005 at the **Cyprus Room**,
Crowne Plaza Cabana, 4290 El Camino Real, Palo Alto, CA 94306.
Telephone: 650-857-0787; FAX: 650-496-1939; Website:
<http://www.cppaloalto.crowneplaza.com/>. Please note the change of
meeting venue.

**Registration**:

Registration is free but required. Contact Leming Shi, National Center
for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079.
Tel: 870-543-7387; <leming.shi@fda.hhs.gov>.