[R] error with the function GOHyperG from GOstats package

[James W. MacDonald]

Sabrina Carpentier wrote:
> I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0,

The release versions of BioC require R-2.0.1. You might try upgrading 
your R version and trying again, because I cannot replicate this error.

Note that if you upgrade to R-2.1.0 (the current version of R), you will 
need to use the development versions of BioC packages (use develOK=TRUE 
in your call to getBioC()). These devel versions of the BioC packages 
are not really that developmental right now, as we are fast approaching 
the release date for BioC 1.6.

Best,

Jim


> 
> and when I use the function GOHyperG, I have the following error:
> 
> w1<-as.list(hgu95av2LOCUSID)
> 
> w2<-unique(unlist(w1))
> 
> set.seed(123)
> myLL<-sample(w2,100)
> 
> xx <- GOHyperG(myLL)
> Error in mget(x, env = GOTERM, ifnotfound = NA) : 
> recursive default argument reference
> 
> In fact first I tried this function with my locusId ' list (with affymetrix hgu133plus2), but I had the same error...
> 
> Any help is appreciated 
> 
> Regards,
> Sabrina
> 
> 
> 
> Sabrina Carpentier
> Service Bioinformatique
> Institut Curie - Bat. Trouillet Rossignol (4e étage)
> 26 rue d'Ulm - 75248 Paris Cedex 5 - FRANCE
> Tel : +33 1 42 34 65 21 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623