[BioC] Affymetrix question

[Jenny Drnevich]

At 07:54 AM 10/26/2005, you wrote:
>lucia García wrote:
> > Hello,
> > I have a question for the analysis of microarays data in affymetrix. It is
> > possible to use the Detection Call (P/A/M) with obtained data with RMA,
> > GCRMA, PLIER or MBEI.
> > Thank you
>
>You *could* use the detection calls with these methods, but I am not
>sure if it would be informative or not. First, these calls don't really
>tell you if the gene is 'present' or not - all they do is tell you if
>the expression of the PM probes appears to be greater than that of the
>MM probes. Given that 30 - 40% of the MM probes are larger than the PMs,
>the utility of the detection calls is questionable.

There is a paper by Choe et al. 2005 
(http://genomebiology.com/2005/6/2/R16) where they created another spike-in 
experiment, except that they derived all the RNAs by PCR; they spiked-in 
about 1300 RNAs at different concentrations and used another ~2500 RNAs at 
equal concentrations as the background RNA population. As far as I'm aware, 
this experiment is unique in that they "knew" all the RNAs that were 
present, and according to their analysis the P/A/M detection call was 
pretty accurate. I don't use MAS5, but I do pre-filter the genes based on 
P/A/M calls in a very conservative way: only if a gene called absent in all 
chips is it thrown out.

That's my 2-cents,
Jenny




>Second, the only method you mention that uses the MM probe data is MBEI
>(and only if you use the PM-MM model). If you are not using the MM probe
>data, how useful is it to know that the PMs are larger than the MMs?
>
>If you are simply trying to remove those genes that appear not to be
>expressed, then you might look at some of the functions in the
>genefilter package, as well as this paper (particularly section 2.1).
>
>http://www.bepress.com/bioconductor/paper7
>
>Best,
>
>Jim
>
>
> >
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>
>--
>James W. MacDonald
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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