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?

Thanks for further help.

Tim







On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao <yuan.x.hao@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.
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>

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