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

[Wang mingyi]

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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