...and by the way, what is your sessionInfo(), i.e. what does the following report?
> library("aroma.affymetrix"); > sessionInfo(); /Henrik On Thu, Apr 5, 2012 at 1:55 PM, Henrik Bengtsson <henrik.bengts...@aroma-project.org> wrote: > Hi, > > first of all, there is a very simple reason for this, we just have to > find out why. My best guess now is that one of the files are > incomplete. Start a fresh R session and verify that you get the > exactly same *file sizes* as below: > >> library("aroma.affymetrix"); >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full"); >> ds <- GenericDataFileSet$byPath(getPath(cdf)); >> print(as.list(ds)); > > [[1]] > GenericDataFile: > Name: GenomeWideSNP_6 > Tags: Full,na31,hg19,HB20110328 > Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl > File size: 7.18 MB (7526452 bytes) > RAM: 0.00 MB > > [[2]] > GenericDataFile: > Name: GenomeWideSNP_6 > Tags: Full,na31,hg19,HB20110328 > Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp > File size: 8.97 MB (9407867 bytes) > RAM: 0.00 MB > > [[3]] > GenericDataFile: > Name: GenomeWideSNP_6 > Tags: Full > Full name: GenomeWideSNP_6,Full > Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.CDF > File size: 470.44 MB (493291745 bytes) > RAM: 0.00 MB > > [[4]] > GenericDataFile: > Name: GenomeWideSNP_6 > Tags: HB20080710 > Full name: GenomeWideSNP_6,HB20080710 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs > File size: 170.92 MB (179217531 bytes) > RAM: 0.00 MB > > /Henrik > > On Thu, Apr 5, 2012 at 5:40 AM, Frederic Foucault > <frederic.fouca...@gmail.com> wrote: >> Hi, >> >> Here is the path >>>path <- getPath(cdf) >>> list.files(path) >> [1] "GenomeWideSNP_6,Full,HB20080710.acs" >> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl" >> [3] "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp" >> "GenomeWideSNP_6,Full.cdf" >> >> Frederic >> >> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit : >>> >>> 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 >>> >>> "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/