On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen <clauslindbj...@gmail.com> wrote: > Hi, > > Last week I ran CRMA (v2): Paired total copy number analysis > > 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 > > Indicating that the mapping is to hg18.....? > Can anyone explain ?
Don't worry, everything in your analysis is correct. It's just that the file generated by CbsModel has "hg18" hard wired in the output. You can manually search-and-replace "hg18" and "hg19" and everything should be as you expected. /Henrik > > 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/ -- 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/
