[BioC] GoStats

[Robert Gentleman]

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.
> 
> 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)
> 
> 
> 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????

 Hi,
  I have updated the return value for the package, I hope that comes
  close to addressing your concerns. 

  GO maps to LocusLink, so it does not make sense for this function to
  start with Affy (or at least I don't think it does). So if you have
  some affy ids, you can use the LOCUSID environment to get the locus
  link values.

  [if you have your affy id's in a vector x, you can go
   y = unlist(mget(x, hgu95av2LOCUSID))
   names(y) = NULL
   byLL = split(x, y) ##gets Affy id by locuslink;]

  Given a unique set of LocusLink IDs you can call GOHyperG, and now
  in the return value you will get a mapping from GO id to all Affy
  IDs, at that probe. You can then use other things - to reduce these
  to unique LocusLink etc)

   So, if we presume the output of GOHyperG is in the variable xx (as
   it will be if you just use exampel(GOHyperG),
   you will now see (or when you get the new version)
 
  > names(xx)
[1] "pvalues"   "goCounts"  "chip"      "go2Affy"   "intCounts" "numLL"    
[7] "numInt"    "intLLs"   

  and now we can use go2Affy to find the GO to LL maps

   myGO2LL = lapply(xx$go2Affy, function(x) unique(unlist(mget(x,
         hgu95av2LOCUSID))))

   I think that gets pretty close to what you wanted, but let me know
   if it is not yet correct.

  Robert
		
> 
> 
> 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                            |
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