[BioC] Problem with GOHyperG

[Bosotti, Roberta [Nervianoms]]

Hi Sean,

thanks for your reply. I downloaded it from Bioconductor site, I guess it is
the latest one. What I realized meanwhile is taht the GOstats package gives
me error messages on the GO and hgu95av2 versions: 

> require(GOstats)
Loading required package: GOstats 
Loading required package: Biobase 
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.
Loading required package: annotate 
Loading required package: RBGL 
Loading required package: genefilter 
Loading required package: multtest 
[1] TRUE
Warning messages: 
1: Your version of hgu95av2 must be at least 1.6.x in: f(libname, pkgname) 
2: You must have package GO version >= 1.6.0 in: f(libname, pkgname)

Regarding GO, I have 1.5.0 version, so that's why. I upgraded to version
1.6.8, but this is not supported by my R version (R1.9.1). Do you know where
I can find GO version 1.6.0? Or where I can download a newer version of R
for Unix?
Regarding Affy annotation file, I'd actually work with the 133plus, so I
suspect that the package do not support the 133plus version (in the release
notes it is suggested the usage of hug95av2). Did it sounds correct to you?

Thanks again

Roberta

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
Sent: Tuesday, January 25, 2005 5:01 PM
To: Bosotti, Roberta [Nervianoms]
Cc: 'bioconductor at stat.math.ethz.ch'
Subject: Re: [BioC] Problem with GOHyperG


Roberta,

My guess is that you are using an older version of GOHyperG.  Install a  
newer version will likely help.

Sean

On Jan 25, 2005, at 10:23 AM, Bosotti, Roberta [Nervianoms] wrote:

> Hi List,
>
> I'm using GOHyperG to calculate pval in hyper geometric test, but I  
> got an
> error message.
>
> Here are the commands I typed:
>
> require(hgu133plus2)
> require(GO)
> require(graph)
> require(GOstats)
> require(annotate)
> my.go<-"BP"
> gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go)
>
> #where gNsLL is a list of LocusLink.
>
> And here is the error message I got:
>
> Error in match.fun(FUN) : Object "Ontology" not found
>
> Can anybody help me in understanding what I'm doing wrong?
>
> Thanks,
>
> Roberta
>
> Roberta Bosotti
> Biology Dep., Genomics Unit
> Nerviano Medical Science s.r.l.
> viale Pasteur 10,
> 20014 Nerviano (MI) - Italy
> roberta.bosotti at nervianoms.com
>
>
>
>
>
>
>
>
>
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