Getting Intensities For Genotype Calling In Axiom Cel Files With Apt
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
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Michael Dondrup
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Genotepes
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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
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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.
It's a very new one, Axiom. I'll check out whether there is already something. thanks