Hi. On Wed, Apr 4, 2012 at 7:57 AM, Fred Foucault <frederic.fouca...@gmail.com> wrote: > Hello, > > I want to get allele specific copy number from SNP6 CL files > I´m following the vignette for ACNE. > I installed the annotation data in \test\annotationData\chipTypes > \GenomeWideSNP6.0
The name of that subdirectory is not correct. Make sure it is *exactly* as shown in the vignette. See also http://aroma-project.org/setup/ What puzzles me though is how you manage to setup the AffymetrixCdfFile object 'cdf' in the first place. You must have done something different than: chipType <- "GenomeWideSNP_6"; cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full"); print(cdf); because that should also give a similar error. /Henrik > > "GenomeWideSNP_6,Full,HB20080710.acs" > "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl" > "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp" > "GenomeWideSNP_6,Full.cdf" > > GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are > from aroma > > here is the error : > gi <- getGenomeInformation(cdf); > Error in getGenomeInformation.AffymetrixCdfFile(cdf) : > [2012-04-04 16:48:48] Exception: Failed to retrieve genome information > for this chip type: GenomeWideSNP_6 > > at #02. getGenomeInformation.AffymetrixCdfFile(cdf) > - getGenomeInformation.AffymetrixCdfFile() is in environment > 'aroma.affymetrix' > > at #01. getGenomeInformation(cdf) > - getGenomeInformation() is in environment > 'aroma.affymetrix' > > > Thank you for your help > Frederic > > -- > 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/
