[BioC] GOstats: get genes for correspondâ ing enriched GO term

[James W. MacDonald]

Hi Tim,

On 7/21/2012 10:25 AM, Lan Sky wrote:
> Hi, Yuan
> Thanks alot for your help.
> I used yeast ORF id as input vectors of geneIds and universeGeneIds.
> These are the summary of GOHyperGResult instance
>
> Gene to GO BP  test for over-representation
> 1660 GO BP ids tested (9 have p<  0.01)
> Selected gene set size: 427
>      Gene universe size: 5616
>      Annotation package: org.Sc.sgd
>
> when I used
>
> ps<-probeSetSummary(over,0.05)
>
> I got warning:
> The vector of geneIds used to create the GOHyperGParamsobject was not a
> named vector.
> If you want to know theprobesets that contributed to this result
> either usea named vector for geneIds, or pass a vector of probeset IDs
> via sigProbesets.
> when I use the input geneIDs (segene) to pass the vector via sgProbesets
> like:
>
> ps<-probeSetSummary(over,0.05,,segene)  //segene is input yeast ORF ID
>
> I still got a empty resut.
> Did I do something wrong?

Well if you actually used the code above, I am surprised it even ran. 
Double commas usually result in an error.

Also, please re-read the message you got from probeSetSummary(). You are 
supposed to be passing in a vector of probeset IDs, not re-sending the 
ORF IDs.

Best,

Jim


>
> Thanks for further help.
>
> Tim
>
>
>
>
>
>
>
> On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao at gmail.com>  wrote:
>
>> Would "probeSetSummary()" do what your want?
>>
>> Yuan
>>
>>
>> On 21 Jul 2012, at 02:47, Tim [guest] wrote:
>>
>>
>>> Hi,
>>>
>>> I used GOstats to perform enrichment test on a set of genes (20).
>>>
>>> There are 7 GO terms with pvalue less than cuttoff and therefore shown in
>>> the result table.
>>>
>>> How can I get the information that which gene in the input gene set
>>> belong to which GO term of these enriched GO terms?
>>>
>>>
>>>
>>>
>>> best,
>>>
>>> Tim
>>>
>>> -- output of sessionInfo():
>>> Thanks for any comments.
>>>
>>> --
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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