Hi, The error message says: "Failed to retrieve genome information for this chip type: GenomeWideSNP_6"
>From your reply to my message in your other thread "Problem with AffymetrixCelSet cmd" it looks like you are indeed missing annotation files. (Currently you only have the cdf, which basically connects each location on the microarray to the corresponding probe idea; but you don't have any information on the location of the probes on the genome, which is why you get the above error message.) Try to follow the CRMAv2 vignette: http://aroma-project.org/vignettes/CRMAv2 step by step. In the "Setup" section of that vignette you will find how to get the other annotation files. And then your analysis should work properly. Note that the 'doCRMAv2' block is essentially a wrapper that executes the preprocessing step described in more detail in the above vignette. Cheers, Pierre On Mon, Jun 18, 2012 at 10:58 PM, NT_CMU <[email protected]> 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 [email protected] > 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
