Hi all,

I was looking over an analysis that was done by someone in my lab in which
the person used the aafTableInt on the raw data (AffyBatch object created by
ReadAffy to save the expression data.
So I was wondering what algorithm does aaTableInt use for summarizing the
probes to probesets, so I looked into the code of
aafTableInt(AffyBatch,probeids=featureNames(AffyBatch)) which really
confused me because in effect it returned
exprs(AffyBatch)[match(probeids,featureNames(AffyBatch)),]
It was my understanding that exprs(AffyBatch) object returned the probe
expression levels and not the probeset summarized expression data, am I
missing something?

 I also noticed that the sum of the pm probes and mm probes is less than the
nrows of the exprs(AffyBatch). Are the rest of the probes just controls?

Thanks in advance,
Achilleas

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