[BioC] filtering on external genelist
James W. MacDonald
jmacdon at med.umich.edu
Tue Sep 11 22:29:57 CEST 2007
> Oleg Moskvin <ovm at ...> writes:
>> I think this should be pretty simple task but I cannot find an appropriate
>> package for that.
>> I need to generate a subset of eSet object which contains certain probesets
>> indicated in an external genelist (outside R environment).
>> I.e. this procedure should look like this:
>> mylist <- read.table .....
>> fltered.eset <- someFunction(eSet, mylist)
>> Probably this is already implemented somewhere.
>> Any hints will be appreciated.
>> All the best,
>> Bioconductor mailing list
>> Bioconductor at ...
>> Search the archives:
> I have the exact same question. I am working with 2-color data in limma
> however. I'd like to be able to make a table of Mvalues corresponding to a list
> of geneIDs from an external table. Any help is appreciated.
That is not the same question, really. Your question should be easily
answered by reading 'An Introduction to R', as that is a simple
The answer to the original question is also pretty simple. I don't know
if this is documented somewhere, but I think the principle of least
surprise applies here:
mylist <- read.table("my_external_list")
filtered.eset <- original.eset[mylist,]
As an example:
> thenames <- featureNames(fibroEset)[sample(1:12625, 300)]
> subsetted.eset <- fibroEset[thenames,]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 300 features, 46 samples
element names: exprs
sampleNames: 1, 2, ..., 46 (46 total)
varLabels and varMetadata:
samp: sample code
species: h: human, b: bonobo, g: gorilla
rowNames: 37599_at, 34494_at, ..., 36333_at (300 total)
varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation  "hgu95av2"
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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