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filtering probesets with Bioconductor?

3 messages · baumeist, Martin Morgan

baumeist
# 
Hi,

I am relatively new to R and Bioconductor and am trying to filter the
topTable that I generated of differentially expressed genes from my
normlized eset file comprised of ~ 40 HG-133A Affy microarrays .  I would
like to see if particular probesets are represented in this list. 
Alternatively I would like to
generate a topTable of differentially expressed genes using only specified
probesets within my eset 
file.

Can anyone tell me how I would  begin to approach this?  I have looked into
using the genefilter() function but can't figure out if it can take the
right parameters (i.e. specific probe set id's).

Thanks in advance,
-M

This is the code I used to generate my topTable
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Martin Morgan
#
On 11/22/2011 02:51 PM, baumeist wrote:
Bioconductor defines classes (like ExpressionSet, the class of your eset 
instance, presumably) which the general R user knows nothing about. It's 
better to ask for help about these questions on the Bioconductor mailing 
list (where you'll also find a community enriched for knowledge about 
Bioinformatics).

   http://bioconductor.org/help/mailing-list/

Perhaps you want to subset eset by the feature names you're interested 
in, along the lines of

   eset1 = eset[featureNames(eset) %in% myFeatures,]

Don't forget to include the output of sessionInfo() and a fully 
reproducible example.

Martin