Getting Intensities For Genotype Calling In Axiom Cel Files With Apt

Question

[Genotepes]

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

[Michael]

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.

[Genotepes]

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

Answer 1

[Michael]

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