[BioC] Problem with GOHyperG

[Sean Davis]

Roberta,

Ah, R-1.9.1 is the issue, I believe.  Bioconductor release 1.5 requires  
at least R-2.0.0, if I'm not mistaken.  You can still get bioconductor  
1.4 release here  
(http://www.bioconductor.org/repository/release1.4/package/html/ 
index.html), but I think it would probably be best to upgrade to  
R-2.0.1 as the ultimate solution.

Sean

On Jan 25, 2005, at 12:52 PM, Bosotti, Roberta [Nervianoms] wrote:

> 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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