[BioC] Run GOHyperG on yeast without specifying a chip

maria at cbm.bio.uniroma2.it maria at cbm.bio.uniroma2.it
Tue Jul 4 12:26:03 CEST 2006

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(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!?



Maria Persico, PhD. student
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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