[BioC] GoStats

Robert Gentleman rgentlem at jimmy.harvard.edu
Sat Oct 9 05:26:58 CEST 2004

On Thu, Oct 07, 2004 at 06:25:45PM +0200, Auer Michael wrote:
> When applying GOHyperG to a series of Locus IDs, the function only reports
> the GO ID and the corresponding frequencies. But what most people want to
> have, when interpreting the GO results is the corresponding Affy IDS which
> map on the different Locus IDs and GO IDS.

  I will add this feature to the next release.
  You will then get the GO ID and the set of LocusLink IDs that are
  mapped to that GO ID. You would then use some other tools (like
  those you suggest below) to find the related Affymetrix (or other
  manufacturer IDs).

> Code I use
> Locusids<-mget(AffyIDS,env=hgu133aLOCUSID)
> /*retrieves the LOCUS LINK IDS from a series of AffyIDS*/
> MF<- GOHyperG(Locusids,lib="hgu133a",what="MF")
> /*reports the occurring Gene Ontologies, the frequencies and the
> hypergeometric p values*/
> How can I get a result of the form
> 1. GO ID, freq (output of GoHyperG)
> 2. GO ID, LOCUS ID (multiple occurring GO IDs)
> 3. LOCUS ID, AFFY ID (multiple occurring LOCUS IDs)
  What you would need to do now, is to take each of the set of
  LocusLink IDs you supplied to the call to GOHyperG, and the output
  set of GO IDs and find which LL's are linked to which GO IDs. This
  is done in GOALLLOCUSID, in GO 1.6.4.

  Finally you would mapp the LLs to whatever manufacturer IDs you
  have. That would be done from the manufacturer specific data

> I know that there is the function hgu95av2GO2ALLPROBES$"GO:0000166"
> which
> retrieves all the probes mapping on a GO, but still it is not the result.
> Ok, one would have to make a for loop and look for the occurring probes in
> the sample. But isn't there a better way????

  I am not sure what you mean by a better way? Nor how it would
  necessarily answer your question.

> Thanks a lot
> Michael Auer
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |

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