Getting intensities using apt-genotype-axiom
Does anyone know how to get intensities files from apt-genotype-axiom used for calling the Affy PMRA chip?
Did not find anything in the manuals. Was the .chp files with previous version.
genotype
assembly
pmra
affymetrix
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s.w.vanderlaan •
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Genotepes
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Did you ever solve this problem? I am interested in this too.
Thanks!