[BioC] How to use detect call in GCRMA (or RMA) analysis?

[Jianping Jin]

You may want to try "mas5calls", a function in the affy package and then 
filter out the probesets with most absent calls.
For example:

PAcalls <- mas5calls(affybatch.obj)

HTH,

JP-

--On Wednesday, December 06, 2006 10:47 PM +0000 Wang mingyi 
<mingyiwang at hotmail.com> wrote:

> Dear all,
>
> I have a question for Affymetrix data analysis by GCRMA (or RMA). From
> the GCRMA (RMA) results, we cannot get detect call information which can
> be returned from MAS5. I think this information are useful when we want
> to perform some downstream t-tests. For example, three replicates (after
> drug) comparing with other three replicates (before drug), if given one
> gene, most detect values are "A" in all these 6 replicates, we will think
> the t-test doesnot make sense. So how to deal with this situation? Can we
> incorporate with detect call information from MAS5?
> Thank you in advance!
>
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##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu