[BioC] Run GOHyperG on yeast without specifying a chip

[James W. MacDonald]

Hi Maria,

maria at cbm.bio.uniroma2.it wrote:
> Hello everyone,
> 
> I'm trying to calculate the probability that 2 YEAST proteins share the 
> same biological process by chance as suggested in the Liu's paper (PMID 
> 15905281); I want a p-value associated to each protein pair in my data 
> set; I would like to use the Bioconductor implementation of GO analysis: 
> in the help page of the GOHyperG I read the following phrase:
> 
> " For S. cerevisiae if the 'lib' argument is set to '"YEAST"' then 
> comparisons and statistics are computed using common names and are with 
> respect to all genes annotated in the S. cerevisiae genome not with 
> respect to any microarray chip."
> 
> this is exactly my case, I don't have a chip. I load the libraries GOstats 
> and YEAST and I choose two common names of two proteins to see if the 
> pipeline works:
> 
>>library(GOstats)
>>library(YEAST)
> 
> 
>>myYCM<-c("RAD24","DMC1")
> 
> 
> At this point I got the following error message:
> 
> 
>>xx<-GOHyperG(myYCM, lib="YEAST", what="BP", universe=NULL)
> 
> Error in length(p at universeGeneIds) - numAtCat :
>          non-numeric argument to binary operator
> 
> I suppose that the problem is the universe; what should I provide as 
> universe value if comparisons and statistics are computed using common 
> names....in the error message I see p at universeGeneIds!?

I don't think that is the problem. I think the common names expected are 
things like "YPL113C"   "YNL055C"   "YKL154W"   "YNR076W" (I believe 
these are the Locus Tags?). If I look up the correct locus tags for your 
genes, things work for me.

 > myYCM<-c("YER173W", "YER179W")
 > xx<-GOHyperG(myYCM, lib="YEAST", what="BP", universe=NULL)
 >

HTH,

Jim


> 
> thanks,
> 
> Maria
> 
> Maria Persico, PhD. student
> http://cbm.bio.uniroma2.it/~maria/
> MINT database group
> Universita' di Tor Vergata, via della Ricerca scientifica 11
> 00133 Roma, Italy
> Tel +39 0672594315 (Supervisor's room)
> Fax +39 0672594766
> Mobile phone: +393479715662
> e-mail maria at cbm.bio.uniroma2.it
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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