Hi Myriam, On Thu, Jun 4, 2009 at 4:38 AM, Myriam <[email protected]> wrote: > > Hi, > > I have done (and seems OK, no error message) the low level analysis of > the GenomeWideSNP_6.0 for preparing the analysis of my Affymetrix > results in 50 samples. > However, I cannot get through the steps of defining the CEL files set. > I have put all the CEL files in rawData/CLP/GenomeWideSNP_6.0 folder. > How should I define the set of CEL files to be analysed and which are > contained in that subfolder? > Tried command: > cs <- AffymetrixCelSet$byName("CLP", cdf=cdf) > but error: AffymetrixCelSet not found
The name of the folder containing the CEL files should match the name of the chip type exactly. In your case it should be rawData/CLP/GenomeWideSNP_6.0 not rawData/CLP/GenomeWideSNP_6 Does this work now ? For future posts: it's better to give the complete R output; In your case aroma.affymetrix probably reports something like: Cannot create AffymetrixCelSet. *No such directory: CLP/GenomeWideSNP_6* which tells you (and us) where the problem comes from. Best, Pierre > > I am a bit lost, as a beginner. Sorry to bother but hopefully one of > you can help me? > > Thanks in advance, > Myriam > > > > --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
