Question: paCalls(affyobject, "DABG/PSDABG") output dimension
1
gravatar for colonppg
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
ADD COMMENTlink modified 4.4 years ago by James W. MacDonald51k • written 4.4 years ago by colonppg30
Answer: paCalls(affyobject, "DABG/PSDABG") output dimension
1
gravatar for James W. MacDonald
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.

ADD COMMENTlink written 4.4 years ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 198 users visited in the last hour