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

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 17 19:09:06 CET 2009


Hi Cheng-Yuan,

Cheng-Yuan Kao wrote:
> Hi,
> 
> We have C. elegans expression data set.
> Do you know what exactly [!is.na(entrezIDs) & !duplicated(entrezIDs)] does?

Yes, and so can you. All you need to do is use the built-in help pages.

?"!"
?is.na
?duplicated

Best,

Jim


> 
> Thanks.
> 
> Cheng-Yuan
> 
> On Tue, Nov 17, 2009 at 3:34 AM, Yuan Hao <yuan.hao at ucd.ie> wrote:
> 
>> 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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>>
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826



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