[BioC] Affymetrix question

[James W. MacDonald]

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.

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