Hi, Last week I <http://aroma-project.org/vignettes/tumorboost-lowlevel><http://aroma-project.org/node/3>ran *CRMA (v2): Paired total copy number analysis*<http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis> Using the following annotation files
GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,monocell.CDF GenomeWideSNP_6,HB20080710.acs The script ran without any problems. But I am a little uncertain about whether the output is mapped to hg18 or hg19 ? As the annotation files are hg19 I expected the output to be so, too. But in the outfile from CBS "regions.xls" all entries are associated url of this format * http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A32255-386024 *<http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A32255-386024> Indicating that the mapping is to hg18.....? Can anyone explain ? Help will be much appreciated !! Claus -- 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/
