[BioC] Rcode for removing probes

[Jenny Drnevich]

Hi Anatole,

It's better to post questions like this to the BioC list, although 
you can copy the specific person you hope will answer.

At 04:49 PM 2/8/2010, you wrote:
>Hi Dr Drnevich,
>My name is Anatole and I work at UCLA. I found your code for 
>removing probes and probesets from affy on Bioconductor help website 
>and I had two questions which I wanted to ask you:
>My first question was should I use your code on raw data before any 
>background correction and normalization or it doesnt matter if I use 
>it on the background corrected and quantile normalized data?

If you want to remove probes and/or probe sets, there is usually a 
specific reason for doing so, such as there are problems with the 
probes/sets. Therefore, you usually remove them prior to any 
normalization. However, if you just want to remove entire probe sets 
because they don't meet some criteria for expression ("filtering"), 
then typically you do that after pre-processing and normalization. 
You don't need to use RemoveProbes to filter - you can just use a 
character vector of the probe set names to subset your ExpressionSet object.

>My second question was if I am interested in removing some probes 
>and some other probesets, do I have to run two seperate commands one 
>for removing probes and one for removing probesets or can I 
>simultaneously remove probes and probesets in one command, meaning 
>running a code as such:
>"removeProbes(listOutProbes = tmp1, listOutProbeSets = tmp2, cleancdf)
>where tmp1 is a character vector of probes to be removed and tmp2 is 
>a character vector of probeset names to be removed

You should be able to remove both probes and probe sets in the same 
call - let me know if it doesn't work. You definitely should not do 
two calls to RemoveProbes(), because once the cdf has been modified 
once, the indexing and subsetting might not work correctly the second time.

Cheers,
Jenny

>
>thanx a lot,
>Anatole
>

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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e-mail: drnevich at illinois.edu