[BioC] Affy: probeset to gene expression with expresso

[James W. MacDonald]

Hi Martin,

None of the functions in the affy package know anything about the 
annotation of the various probesets, so there is no facility there to 
summarize at anything but the probeset level.

However, you could use one of the MBNI remapped probesets, which 
pre-aggregate the probes into probesets based on a few different 
annotation databases.

Best,

Jim



On 8/13/2013 11:38 AM, Martin Preusse wrote:
> Hi Jim,
>
> thanks, this is a very clever (and R like) way to average the expressions on the expression matrix. In my example this would work for 'exprs(eset)' when I replace the probe set ids with gene symbols.
>
> Still, it would be great to know if can be achieved with a convenience function (e.g. expresso).
>
> Martin
>
>
> Am Dienstag, 13. August 2013 um 17:28 schrieb James W. MacDonald:
>
>> Hi Martin,
>>
>> I just answered a very closely related question. See if this helps:
>>
>> https://stat.ethz.ch/pipermail/bioconductor/2013-August/054353.html
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On 8/13/2013 9:47 AM, Martin Preusse wrote:
>>> I am trying to get the gene level expression values from an Affy micro array, i.e. merge the values for probe sets representing the same gene.
>>>
>>> I tried to use the 'expresso' function from the affy package, but I always end up with an ExpressionSet containing probe sets, not genes.
>>>
>>> What is an easy way to summarize/merge probe sets to (entrez) genes?
>>>
>>>
>>> library(affydata)
>>> library(affy)
>>>
>>> # get the 'Dilution' affy batch
>>> data(Dilution)
>>>
>>> eset<- expresso(Dilution, bgcorrect.method='rma',
>>> normalize.method='constant',
>>> pmcorrect.method='pmonly',
>>> summary.method='avgdiff')
>>>
>>>
>>> write.exprs(eset,'testfile.txt')
>>>
>>>
>>> P.S.: I know it might not be the best idea to average probe sets, but I would like to try ;)
>>>
>>> Cheers
>>> Martin
>>>
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>>
>>
>> -- 
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099