On Wed, Jun 27, 2012 at 9:09 AM, Andrew <andysure...@gmail.com> wrote: > thanks Henrik. > > The output is: > > [1] "GenomeWideSNP_6,Full.cdf" > [2] "GenomeWideSNP_6,HB20080710.acs" > [3] "GenomeWideSNP_6,na31,hg19,HB20110328.ufl" > [4] "GenomeWideSNP_6,na31,hg19,HB20110328.ugp"
For "GenomeWideSNP_6,Full.cdf", you need (=missing): "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl" "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp" For "GenomeWideSNP_6.cdf", you need/have: "GenomeWideSNP_6,na31,hg19,HB20110328.ufl" "GenomeWideSNP_6,na31,hg19,HB20110328.ugp" "GenomeWideSNP_6,HB20080710.acs" is the same for both CDFs. /Henrik > > > > On Tuesday, June 26, 2012 11:51:49 PM UTC-4, Henrik Bengtsson wrote: >> >> Following the troubleshooting of annotationData/ on >> http://aroma-project.org/troubleshooting/DirectoryStructures using >> chipType <- "GenomeWideSNP_6", what does print(list.files(path=path)) >> output? >> >> /Henrik >> >> On Tue, Jun 26, 2012 at 8:04 PM, Andrew <andysure...@gmail.com> wrote: >> > I feel it might be better to post my question in this thread, as I have >> > encountered the same error. >> > >> > I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the >> > Full cdf file from Affymetrix. And I still got the same kind error >> > NT_CMU >> > got for "getGenomeInformation". >> > >> > Could you please give me a hint, where should I look for? Thanks! >> > >> > >> > On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote: >> >> >> >> Hi >> >> >> >> I'm trying to run the command "doCRMAv2", and i get these errors. Let >> >> me >> >> know what the problem is, if any of you have encountered this before. I >> >> thought i did not have some library installed but, i have both ACNE and >> >> aroma.affymetrix working properly. >> >> >> >> > ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full") >> >> Error in getGenomeInformation.AffymetrixCdfFile(cdf) : >> >> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information >> >> for >> >> this chip type: GenomeWideSNP_6 >> >> >> >> at #12. getGenomeInformation.AffymetrixCdfFile(cdf) >> >> - getGenomeInformation.AffymetrixCdfFile() is in environment >> >> 'aroma.affymetrix' >> >> >> >> at #11. getGenomeInformation(cdf) >> >> - getGenomeInformation() is in environment 'aroma.affymetrix' >> >> >> >> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this) >> >> - getSubsetToAvg.AllelicCrosstalkCalibration() is in >> >> environment >> >> 'aroma.affymetrix' >> >> >> >> at #09. getSubsetToAvg(this) >> >> - getSubsetToAvg() is in environment 'aroma.affymetrix' >> >> >> >> at #08. getParameters.AllelicCrosstalkCalibration(this) >> >> - getParameters.AllelicCrosstalkCalibration() is in >> >> environment >> >> 'aroma.affymetrix' >> >> >> >> at #07. getParameters(this) >> >> - getParameters() is in environment 'R.rsp' >> >> >> >> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose) >> >> - process.AllelicCrosstalkCalibration() is in environment >> >> >> >> >> >> Thanks >> >> >> >> Nitesh >> > >> > -- >> > 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/ -- 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/
