[BioC] GoHyperG

[Katleen De Preter]

Thank you for your answer,
however I want the program automatically add a column to my table with 
the gene symbols that correspond to the most significant GO terms?
So I don't want to do it for every GO manually.
Best regards,
Katleen

Robert Gentleman wrote:

> If what you want is the mapping from some manufacturer's identifiers 
> to  gene symbols (?) then
> you need to use the data packages (if you are using affy then you get  
> the one for your chip, if not, then you have more work to do, but you  
> didn't really give us very much to go on here)
>
> So, for example, if I had some affy ids from a HG-U95a2 chip, in a  
> vector x,
> I would do something like
>
> library(hgu95av2)
> mysyms = unlist(mget(x, hgu95av2SYMBOL))
>
> if what you want is to first, find all genes that have a GO 
> annotation,  given a chip you can use
> the mappings in hgu95av2GO2PROBE or hgu95av2GO2ALLPROBES (and I will  
> leave it to you to read the manual pages and find out what the  
> difference is)
> eg.
> > hgu95av2GO2ALLPROBES$"GO:0000022"
>        TAS
> "37171_at"
>
> and then
>  > hgu95av2SYMBOL$"37171_at"
> [1] "KIF23"
>
> Robert
>
> On Feb 24, 2005, at 6:53 AM, Katleen De Preter wrote:
>
>> Dear colleagues,
>> I have a little question about managing data from the GoHyperG  
>> function.
>> I would like to obtain a table with the 20 most significant  BP-GO  
>> terms of a genelist (obtained with SAM), the p-values, the 
>> discription  of the GO term and a column with the gene-names 
>> (comma-separated) from  the genelist that belong to these GO terms. 
>> How can I obtain this last  column???
>>
>> I managed to obtain the 3 first columns with:
>> GOtest<-GOHyperG(genelist,what="BP")
>> table<-data.frame(sort(GOtest$pvalues)[1:t],GOtest$intCounts[1: 
>> t],goterms[rownames(as.matrix(GOtest$intCounts[1:t]))])
>>
>> Thank you in advance!
>> Katleen De Preter
>>
>>
>>
>> -- 
>> No virus found in this outgoing message.
>> Checked by AVG Anti-Virus.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>
> +----------------------------------------------------------------------- 
> ----------------+
> | Robert Gentleman              phone: (206) 
> 667-7700                             |
> | Head, Program in Computational Biology   fax:  (206) 667-1319   |
> | Division of Public Health Sciences       office: 
> M2-B865                     |
> | Fred Hutchinson Cancer Research 
> Center                                          |
> | email: 
> rgentlem at fhcrc.org                                              
>                          |
> +----------------------------------------------------------------------- 
> ----------------+
>

-- 
*dr. ir. Katleen De Preter*
Center for Medical Genetics Ghent (CMGG)
Ghent University Hospital
Medical Research Building (MRB), 2nd floor, room 120.038
De Pintelaan 185, B-9000 Ghent, Belgium
+32 9 240 5533 (phone) | +32 9 240 6549 (fax)
http://medgen.ugent.be
Katleen.DePreter at UGent.be <mailto:Katleen.DePreter at UGent.be>


-- 
No virus found in this outgoing message.
Checked by AVG Anti-Virus.