I am using aroma.affymetrix for pre-processing of data for CNV analysis. Briefly, I normalize and estimate copy number with CRMAv2. I use the calculated copy number along with the chromosomal locations from the ugp file to run CBS using segment from the DNAcopy package. Then I analyze the segmented copy number calls with downstream software like RAE from MSKCC.
I am analyzing data collected on the GWS6 platform. I am getting errors when multiple probes map to the same genomic location. For example, probe SNP_A-8462292 and probe CN_1173216 both map to chromosome 6 locus 29837188. Is this behavior expected? Is there a work around for this issue? Thanks, Mike -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
