Hi,

We have C. elegans expression data set.
Do you know what exactly [!is.na(entrezIDs) & !duplicated(entrezIDs)] does?

Thanks.

Cheng-Yuan

On Tue, Nov 17, 2009 at 3:34 AM, Yuan Hao <yuan.hao@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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> ----------------------------------------------------------------------
>> Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, München D
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>

	[[alternative HTML version deleted]]

