![](media/image1.jpeg){width="1.0791666666666666in"
height="0.26458333333333334in"}Summary of the MAQC **February-23-2006**
Teleconference

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

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

Teleconference Date: February 23, 2006 (9 am PST/11 am CST/12 pm
EST/17:00 GMT)

Summary Date: February 24, 2006

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.  **Flags and Offset Values**: Manufacturers' latest (additional)
    instructions for handling flags and offset values have been posted
    for download (FlagsOffsetHandling.zip).

2.  **V2_norm_ILM**: Adding an extra offset value of 15 based on the
    originally distributed ILM data; has been posted for download.

3.  **V2_norm_GEH**: (1) Adding an offset value of 0.3 to each data
    point; (2) The request of GEH and GEH_2 for replacing old GEH_2 data
    with new data was extensively discussed and approved. According to
    Rick Jensen and Rich Shippy, the old GEH_2 data were generated with
    protocols that significantly deviated from GEH's recommended SOP's
    for the MAQC project. Such deviations included the use of a wrong
    dye (SA-Alex instead of SA-Cy5) and a wrong washing solution (water
    instead of 0.1x SSC). In addition, Rick provided a PowerPoint slide
    that clearly demonstrated the dramatic decay of signal intensity
    during the scanning process while the old GEH_2 data were collected
    in September 2005, a strong indication of the effect of ozone. GEH_2
    site repeated 20 arrays and collected new data on February 17, 2006
    by exactly following the GEH recommended SOP's for the MAQC project
    and submitted the new data to FDA/NCTR on the same day. Because of
    the obvious problems with the old GEH_2 data and the availability of
    the new GEH_2 data that were generated by following the GEH SOP's
    and the fact that there will be no additional delay in final data
    analysis, the majority of the MAQC group on the TC approved the
    request for replacing new GEH_2 data for MAQC data analysis.
    However, it was also agreed that in the main manuscript we should
    clearly state the importance of following manufacturer's SOP's and
    what exactly happened to the old GEH_2 data, which will also be made
    publicly available along with other MAQC data. Therefore, the new
    GEH_2 data should be used in all MAQC data analysis. The V2_norm_GEH
    data set has been posted for download.

4.  **One-One Sequence-mapping Table**: The MAQC group greatly
    appreciated the efforts of the NCBI team (Jean, Danielle, and Damir)
    for creating a comprehensive probe sequence mapping table with
    different categories of mapping quality (the file,
    MAQC_mapping_2006_02_19.zip, can be downloaded from MAQC data
    download site). Such information will be very helpful for people to
    explain the discrepancies that may exist across different platforms.
    However, data analysis sites expressed strong desire of using a
    simple, one-one mapping table so that an overview of cross-platform
    comparability can be easily obtained. The one-one mapping table
    distributed by Rick before Palo Alto meeting was based on using
    3'-closeness as the major criterion to pick one probe (or probe set)
    from multiple perfect matches, a criterion previously agreed upon by
    all manufacturers and confirmed again during the TC. The MAQC group
    decided to continue to use a cleaned-up version (by removing 47
    redundant records) of the one-one mapping table originally provided
    by Rick for any cross-platform data comparison across all
    manuscripts except for MS-5 (the mapping paper). The new table
    (reference_mapping.zip, with 14885 records for ABI, AFX, AG1 (AGL),
    GEH, ILM, NCI, and TAQ) is ready for download. Mapping tables for
    EPP, GEX, and QGN can be found in EPP_GEX_QGN_reference_mapping.zip.

5.  **Manuscripts**: Each manuscript team leader was sent instructions
    (along with the current publication plan) to submit an initial draft
    (or very detailed outline with description on the types of
    figures/tables) to its team members (and copy to Leming Shi) by
    mid-night Tuesday, Feb-28-2006. A manuscript topic will be
    automatically eliminated from the publication plan for any further
    consideration for submission to *Nature Biotechnology* if the
    deadline is not met. The e-mail (and the plan) was also forwarded to
    the primary contact from official platform providers, RNA providers,
    and official data analysis sites.

6.  **Others**: Summaries for TCs (Jan-12-06, Jan-26-06, and Feb-9-06)
    and Boston meeting have been posted at the MAQC web site.

Next Teleconference:

**Thursday, March 9, 2006** (9 am PST / 11 am CST / 12 pm EST / 17:00
GMT)

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