[R] filtering probesets with Bioconductor?

Martin Morgan mtmorgan at fhcrc.org
Wed Nov 23 01:02:20 CET 2011

On 11/22/2011 02:51 PM, baumeist wrote:
> 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
>> fit<- lmFit(eset, design)

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 


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.


>> cont.matrix<- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design)
>> fit2<- contrasts.fit(fit, cont.matrix)
>> fit2<- eBayes(fit2)
>> topTable(fit2, number=100, adjust="BH")
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