I am really sorry for asking questions while at the same time has not been contributing to addressing people's issues.
But here yet another issue while I am using the oligo package
dabgps <- paCalls(affyobject, method="PSDABG")
I wonder if I can get gene level readout for presence/absence of the same gene:
> dim(dabg)  861493 221 > dim(dabgps)  257430 221
because this is way more than what I have for gene level read out... even for dabgps, which is probeset level
the manual said "of dimension length(unique(probeNames(object))) x ncol(object) if method="PSDABG") with p-values for P/A Calls."
length(unique(probeNames(affyobject)))  33297
how can I resolve this difference?