Hi Jenny, I run the code through 3 different datasets (each consists of 50-60 U133a cel files), the first 2 datasets run pretty smoothly, the last one has the error msg: Error in ans[[i]][, i.probes] : incorrect number of dimensions Not sure what's causing the problem, but the last one has the largest number of masked probes/probesets: ~179k masked probes (out of 247965 in total) and ~15k masked probe sets (out of 22283 in total). Does the code have a limit on the number of masked probe/probesets? or there are certain probes/probe sets that can not be filtered? Thanks a lot, -Jack On Tue, Aug 31, 2010 at 5:57 PM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Jack, > > It's best to also post your question to the BioC list. First of all, you > link was to the September 2006 code, but there was an update to the code in > September 2008 (I think it still should work): > > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > > Did you see this more recent post on the BioC list about removing > individual probes? The individual probe names have to be in the correct > format, and your's aren't: > https://stat.ethz.ch/pipermail/bioconductor/2010-January/031463.html > > > HTH, > Jenny > > > At 11:46 AM 8/31/2010, you wrote: > > Hi Jenny, > > I am a BioC user and find the following link: > https://stat.ethz.ch/pipermail/bioconductor/2006-September/014242.html > > which is related to removing probes/probe sets from the cdf. It's highly > related to my work, which needs to perform normalization after filtering out > some probe pairs whose PM is not significantly higher than MM. > > I played around with the code in the above link by following the > instruction, it works perfectly when some given probe sets need to be taken > out, but have some problem when some probes (not whole probe sets) need to > be taken out. I am wondering do you have an example for taking some probes > as well as probe sets? I have not figured out what's the correct input for > probes. > > I tried the following inputs and neither of them works. > > maskedprobeSets = rownames(exprs(justRMA(filenames = celfiles)))[1:100] # > this format works > > maskedprobes = rownames(pm(AffyBatch))[1:500] # doesn't work > maskedprobes = as.character(1:500) # doesn't work > > RemoveProbes(listOutProbes=maskedprobes, listOutProbeSets=maskedprobeSets, > cleancdf) > > > Thanks a lot! Your help will be highly appreciated. > > -Jack > > [[alternative HTML version deleted]]