Hi. On Mon, Mar 19, 2012 at 12:02 PM, Fong <fongchunc...@gmail.com> wrote: > Hi, > > I am using SNP6 arrays right now and I've got an annotationData directory > that looks like this: > > GenomeWideSNP_6,Full.cdf > GenomeWideSNP_6,Full,monocell.CDF > GenomeWideSNP_6,HB20080710.acs > GenomeWideSNP_6,Full,na24,hg18,HB20080214.ugp > GenomeWideSNP_6,Full,na24,hg18,HB20080214.ufl > GenomeWideSNP_6,Full,na26,hg18,HB20080821.ugp > GenomeWideSNP_6,Full,na26,hg18,HB20080821.ufl > > Essentially I have the na24 and na26 .ugp and .ufl files. Now when I run > the code: > > library('aroma.affymetrix') > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") > > print(gi) > > UgpGenomeInformation: > Name: GenomeWideSNP_6 > Tags: Full,na24,hg18,HB20080214 > Full name: GenomeWideSNP_6,Full,na24,hg18,HB20080214 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na24,hg18,HB20080214.ugp > File size: 8.97 MB (9407568 bytes) > RAM: 0.00 MB > Chip type: GenomeWideSNP_6,Full > > It seems to always look for the first .ugp file which ends up being the > na24.
Yes, it returns the first matching UGP file, where it search files in lexicographic ("alphabetic+numeric") order. > I've tried to give it tags by going > > gi <- getGenomeInformation(cdf, tags='Full,na26,hg18,HB20080821') That argument 'tags' will be ignored. I'll add it to the to do list, to see if it should/could be supported. > > But it still defaults to na24. Is there a way to keep the annotation files > in the same directory, but tell aroma.affymetrix to use a different set of > annotation files for SNP6 arrays? You can do as follows: library("aroma.affymetrix") cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") gi <- UgpGenomeInformation$byChipType(getChipType(cdf), tags="na31,hg19,HB20110328"); setGenomeInformation(cdf, gi); such that getGenomeInformation(cdf) returns what you wish. Hope this helps /Henrik > > Thanks, > > Fong > > -- > 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/