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>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

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