Question: Getting Intensities For Genotype Calling In Axiom Cel Files With Apt
2
gravatar for Genotepes
8.7 years ago by
Genotepes950
Nantes (France)
Genotepes950 wrote:

Hi,

I have .CEL files and using APT (instead of Genotyping Console). Because I'd like to keep all under Linux, I am trying to extract the intensities information per probeset. I could only get the intensities per probe. Any idea of how to get easily the information

probeset Allele A intensity Alelle B intensity or at least what is called the strength and the contrast ?

Christian

affymetrix snp genotyping • 2.7k views
ADD COMMENTlink written 8.7 years ago by Genotepes950

What is the name of your chip design? Because if there is an annotation package in Bioconductor for it, you should be able to access the probe and probeset intensities.

ADD REPLYlink written 8.7 years ago by Michael Dondrup47k

It's a very new one, Axiom. I'll check out whether there is already something. thanks

ADD REPLYlink written 8.7 years ago by Genotepes950
1
gravatar for Michael Dondrup
8.7 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

The oligo package in Bioconductor might help, here is a tutorial for SNP arrays: http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/doc/V3AffySnpGenotype.pdf

ADD COMMENTlink written 8.7 years ago by Michael Dondrup47k
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