Hi, I have been using the function combineAffyBatch (match probes library) to combine the data for two mouse chips MOE430v2 (45101 probesets) and its subset chip MOE430Av2 (22690 probesets). According to Affymetrix the 22690 probesets in MOE430Av2 are identical in MOE430v2. I ran the following: res <- combineAffyBatch(list(Data.430v2, Data.430Av2),c("mouse4302probe", "mouse430a2probe"), newcdf="comb") comb <- res$cdf This gave a combination expression set with 22702 probesets (ie 12 more probeset names than the subset chip MOE430Av2). I looked to see the number of oligos matching in the different probesets prs <- mget(ls(comb), comb, ifnotfound=NA) nrprobes <- sapply(prs, function(x) nrow(x)) table(nrprobes) > table(nrprobes) nrprobes 1 2 3 4 5 8 9 10 11 20 21 7 2 1 1 1 1 4 11 22631 40 3 The probeset names that were not present on MOE430v2 all had less than 8 oligos matching between the chip types. I was wondering if anyone knew the best way to exclude such probesets in the expression set, or how to avoid this problem in the first place. Thanks and Regards Dr Margaret Gardiner-Garden

Hi Margaret, if you know in the first place that so many probesets are identical, and which ones, you could try to put the AffyBatches together yourself based on that information, using the MOE430Av2 CDF. The main intention of the combineAffyBatch function is for situations where the correspondence between the chips is more complicated, that's why its output is as it is. You could use "rm(..., envir=comb)" to delete the probesets that you don't like from the result of combineAffyBatch. Hope this helps, best wishes Wolfgang Gardiner-Garden wrote: > Hi, I have been using the function combineAffyBatch (match probes library) > to combine the data for two mouse chips MOE430v2 (45101 probesets) and its > subset chip MOE430Av2 (22690 probesets). > According to Affymetrix the 22690 probesets in MOE430Av2 are identical in > MOE430v2. > > I ran the following: > res <- combineAffyBatch(list(Data.430v2, Data.430Av2),c("mouse4302probe", > "mouse430a2probe"), newcdf="comb") > comb <- res$cdf > > > This gave a combination expression set with 22702 probesets (ie 12 more > probeset names than the subset chip MOE430Av2). > > I looked to see the number of oligos matching in the different probesets > prs <- mget(ls(comb), comb, ifnotfound=NA) > nrprobes <- sapply(prs, function(x) nrow(x)) > table(nrprobes) > > > >>table(nrprobes) > > nrprobes > 1 2 3 4 5 8 9 10 11 20 21 > 7 2 1 1 1 1 4 11 22631 40 3 > > > > The probeset names that were not present on MOE430v2 all had less than 8 > oligos matching between the chip types. > > I was wondering if anyone knew the best way to exclude such probesets in the > expression set, or how to avoid this problem in the first place. > > > Thanks and Regards > Dr Margaret Gardiner-Garden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber