Hi Aedin, Aedin wrote: > Thanks for the info on my last question. Can I please ask another ;-)) > > What do you recommend to use when mapping IMAGE ID's and Affy ID's. > UniGene and locus link are returning some very strange results (not a > surprise really :-)). > It depends a lot on what you are trying to do. If you are trying to combine different data sets, then you probably want to match on sequence - which sounds like what you are suggesting below. You might also want to look at MergeMaid, and accompanying papers, as they have an interesting approach that might help. I don' think that there is an example of taking a sequence, say for a cDNA and then finding whether a corresponding affy probe set map to a similar region, but once you are done I'm sure you will contribute one :-) I would use Biostrings, and the corresponding Affy probe package - and do exact matching. If you end up with many-to-many or many-to-one matches I would match them all and then pick the best one. some code snippets, library(annotate) library(hgu95av2probe) ##here you would use the Acc. Num for the gen of interest myseq = getSEQ("D45132") ##here you would use the Affy probe id, for the putative match wp= hgu95av2probe$Probe.Set.Name == "316_g_at" myPr = hgu95av2probe[wp,] nchar(myseq) library(Biostrings) mybs = NucleotideString(myseq, "DNA") ##do this once for each of the probes - and count how many actually ##match match1 = matchDNAPattern(as.character(myPr[1,1]), mybs) as.matrix(match1) Does that help? Robert > I know match probes maps between Affy batches. Can I load IMAGE > sequences into this to map to a Affy cdf package. Is there any example > of this in the BioC help? > > Thanks again BioC for all your help, > Aedin > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >