[BioC] problem with hgu133a // GOstats // BioC-R2.1.1

John Zhang jzhang at jimmy.harvard.edu
Tue Aug 2 15:40:49 CEST 2005

>Where can I find the graph package (I haven't found it on the CRAN website)?

You can get the graph package from Bioconductor.

>*question 2: hgu133a*
>Is it possible that the hgu133a package is not up to date: for example 
>when I give the command aafSymbol("213268_at","hgu133a") following 
>results appear:
>/*PER3 */when I use R 2.1.1 (with recent installation of BioC: 
>getBioC()) and */UTS2/* when I use R 2.0.1 (with recent installation of 
>BioC: getBioC("all")). However, on the Ensembl website 213268_at = 

We rely on NCBI for annnotation. 213268_at is annotated to Z98884 by Affymetrix 
and UniGene says it is PER3.

>Another error message appears with R 2.0.1 when I give the command: 
> >aafSymbol("213268_at","hgu133a"):
>Loading required package: reposTools
>[1] "_You have package hgu133a but the incorrect version_"
>An object of class "aafList"
>An object of class "aafSymbol"
>[1] "UTS2"
>*question 3: BioC-R2.1.1*
>The commands Install or  Update packages from Bioconductor  under the 
>Packages menu-command-bar is not available anymore in the R2.1.1 version 
>compared to the R2.0.1 version? Is it normal or did I forgot something 
>when I installed BioC or R?
>Thank you in advance,
>Best regards,
>*dr. ir. Katleen De Preter*
>Center for Medical Genetics Ghent (CMGG)
>Ghent University Hospital
>Medical Research Building (MRB), 2nd floor, room 120.038
>De Pintelaan 185, B-9000 Ghent, Belgium
>+32 9 240 5533 (phone) | +32 9 240 6549 (fax)
>Katleen.DePreter at UGent.be <mailto:Katleen.DePreter at UGent.be>
>	[[alternative HTML version deleted]]
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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