[BioC] Is there a package or a way to convert "probesets" to "genes"

[Yuan Hao]

Hi Richie,

I am not sure which data set and annotation package you are working  
on, taking hgu133plus2 chip for example. if you just want to get  
Entrez genes corresponding to your probesets, you can simply do:

library("hgu133plus2.db")
entrezIDs<-unlist(mget(probesets, hgu133plus2ENTREZID))
entrezIDs<-entrezIDs[!is.na(entrezIDs) & !duplicated(entrezIDs)]

Hope it is what you want.

Cheers,
Yuan



On 17 Nov 2009, at 08:15, Tobias Straub wrote:

> hi richie,
>
> one easy way to handle the multiple probesets per gene problem is to  
> keep only the one probeset with the highest variance across  
> replicates. the 'nsFilter' function in the 'genefilter' package  
> provides this operation for ExpressionSet objects.
> using this filter approach you might of course miss some  
> differentially regulated splicing events.
>
> best regards
> tobias
>
>
> On Nov 17, 2009, at 12:01 AM, Cheng-Yuan Kao wrote:
>
>> Hi, there,
>>
>> I have a question regarding Affy chip data.
>>
>> We did many expression arrays and used LIMMA to get the  
>> differentially
>> expressed "genes" (control vs treatment).
>>
>> However I found that some probesets have multiple genes according  
>> to Affy
>> annotation file.
>>
>> On the other hand, multiple probesets could match to the same gene.
>> Even more, some probesets matched to the same gene could be  
>> regulated in
>> different way.
>>
>> So actually what LIMMA gave us is differentially expressed  
>> "probesets".
>>
>> Say we have 500 probesets up-regulated but we indeed want to know  
>> how many
>> "genes" are up-regulated.
>>
>> I don't know how to reasonably convert the probesets to genes due  
>> to the
>> non-one-to-one relationship.
>>
>> What's the convention in the microarray field?
>>
>> Any suggestion would be greatly appreciated.
>>
>>
>> Richie
>>
>> 	[[alternative HTML version deleted]]
>>
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>
> ----------------------------------------------------------------------
> Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, München D
>
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