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

[James W. MacDonald]

On 7/21/2012 9:43 PM, Lan Sky wrote:
> Hi, Jim
> Thanks for your information.
> I actually don't have any probesetID.
> I only used yeast ORF id to perform the GO.
> Do I need to do some mapping from ORF to probeset?
> In the message I got, it says, "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."
> "either use a named vector for geneIds."
> what is that supposed to be the input?
>
> Dose it mean geneId instead of probeset?

It depends on how you did things. You have been pretty cryptic about 
what you have done, so we have to read between the lines. In general, 
people use microarray data to do GO analyses. In which case the genes 
are interrogated by one or more 'reporter' molecules, which if the 
manufacturer is Affymetrix, are called probesets.

When you have a significant GO term, one might want to know which of the 
significant reporter molecules contributed to that result. So in the 
case of an Affy analysis, you would pass in a vector of probeset IDs. So 
if you don't have Affy data, then I assume you have some other 
manufacturer IDs you could use. Perhaps you could feed in gene IDs, but 
that wasn't the original intent, and may not work.

Best,

Jim


> Thanks,
> Tim
> On Sat, Jul 21, 2012 at 1:16 PM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     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
>         <mailto: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
>
>

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