Question: paCalls(affyobject, "DABG/PSDABG") output dimension
1
4.4 years ago by
colonppg30
United States
colonppg30 wrote:

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!

oligo pacalls • 691 views
modified 4.4 years ago by James W. MacDonald51k • written 4.4 years ago by colonppg30
1
4.4 years ago by
United States
James W. MacDonald51k wrote:

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.