[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 
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

>> cont.matrix<- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design)
>> fit2<- contrasts.fit(fit, cont.matrix)
>> fit2<- eBayes(fit2)
>> topTable(fit2, number=100, adjust="BH")
>
> --
> View this message in context: http://r.789695.n4.nabble.com/filtering-probesets-with-Bioconductor-tp4097747p4097747.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793



More information about the R-help mailing list