Re: [R] error with the function GOHyperG from GOstats package

From: James W. MacDonald <jmacdon_at_med.umich.edu>
Date: Thu 05 May 2005 - 00:35:24 EST

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]]
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

-- 
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

______________________________________________
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Received on Thu May 05 00:50:41 2005

This archive was generated by hypermail 2.1.8 : Fri 03 Mar 2006 - 03:31:35 EST