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")
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