Hi Jake.
As a starting point, you might have a look at: http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-scratch In there is a script called 'flat2Cdf.R' that takes a flat file of probe information (X/Y location on the chip, probe sequence, identifiers) and creates a CDF file. I assume you will have this information or can get it. Maybe create 2 such flat files. Alternatively, you should also search the Bioconductor archives. I do recall some discussion on this awhile back and there were some scripts generated that removed probes from CDF environments. In any case, you could also familiarize yourself with the CDF format by taking an existing CDF file and reading it in with readCdf() from the 'affxparser' package. That is always good information to know. As far as I can tell, you won't need to modify anything in the CEL files, you'll just have read from the CEL file twice, once from your SNP-probes-removed CDF file and once from SNP-probes-only CDF file. Hope that helps. Mark > > Hi everyone, > > I'm trying to perform probe level analyses on the HG-U133Plus2 chip > data. Basically I have a set of SNPs that overlap with probes from the > chip. I wanted to analyze two different aspects of these "allele- > specific" probes: > > 1) Analyze the probesets without the allele-specific probe > 2) Analyze the allele-specific probe individually > > How do I generate custom CDFs for this purpose? Are the only changes > that need to be made in the CDF or does one have to modify, say, CEL > files as well? > > Any help would be appreciated. > > Thanks, > > Jake > > > > --~--~---------~--~----~------------~-------~--~----~ 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 aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
