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

Tobias Straub tstraub at med.uni-muenchen.de
Tue Nov 17 09:15:19 CET 2009


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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