To clarify, one segment ends at 29837188, the next starts at 29837188. On Friday, September 14, 2012 5:10:00 PM UTC-4, Mike wrote: > > Henrik, > > I am getting errors when running the RAE algorithm from MSKCC due to the > fact that there are multiple probes that map to the same locus. It throws > off the count of the algorithm when there are segments that start and end > at the same locus with different CN calls. This causes the algorithm to > error out because I end up with vectors of different lengths. > > Can you suggest a reasonable work around? Only use SNP probes for these > locations? Take median CN for probes mapping to same location? > > Thanks, > Mike > > On Friday, September 14, 2012 5:00:42 PM UTC-4, Henrik Bengtsson wrote: >> >> On Fri, Sep 14, 2012 at 1:57 PM, Mike <michael...@gmail.com> wrote: >> > 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? >> >> Yes, for some probes the Affymetrix annotation happens to have the >> exact same genomic location. The DNAcopy implementation of CBS is >> what generates those warnings (they are *not* errors). They will not >> cause an issue. >> >> /Henrik >> >> > >> > 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-af...@googlegroups.com >> > To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ >> >
-- 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/
