Dear all:

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

dabg<-paCalls(affyobject, method="DABG")

dabgps <- paCalls(affyobject, method="PSDABG")

I wonder if I can get gene level readout for presence/absence of the same gene:

> dim(dabg)
[1] 861493    221
> dim(dabgps)
[1] 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."

while 

length(unique(probeNames(affyobject)))
[1] 33297

how can I resolve this difference?

Thanks!

PSDABG gives calls at the probeset level, not the transcript level. You cannot do calls at the transcript level using oligo. If you want that, you have to use xps.