[BioC] filtering on external genelist

[James W. MacDonald]

D wrote:
> Oleg Moskvin <ovm at ...> writes:
> 
>> Colleagues,
>>
>> 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,
>>
>> Oleg
>>
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>>
> 
> 
> 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 
subsetting problem.

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:

 > library(fibroEset)
 > data(fibroEset)
 > thenames <- featureNames(fibroEset)[sample(1:12625, 300)]
 > subsetted.eset <- fibroEset[thenames,]
 > subsetted.eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 300 features, 46 samples
   element names: exprs
phenoData
   sampleNames: 1, 2, ..., 46 (46 total)
   varLabels and varMetadata:
     samp: sample code
     species: h: human, b: bonobo, g: gorilla
featureData
   rowNames: 37599_at, 34494_at, ..., 36333_at (300 total)
   varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
   pubMedIds: 12840040
Annotation [1] "hgu95av2"

Best,

Jim


> 
> Thanks,
> 
> D
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623