An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050802/ 8e17590f/attachment.pl

>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 = >*/CAMTA1/*. 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" >[[1]] >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, >Katleen > >-- >*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) >http://medgen.ugent.be >Katleen.DePreter at UGent.be <mailto:katleen.depreter at="" ugent.be=""> > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

> *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? The menu bar has changed. First you click a menu item under packages button to set a repository, then you click the install packages button to get the list of packages from that repository.

>X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >Date: Tue, 02 Aug 2005 20:00:23 +0200 >From: Uri David Akavia <uridavid at="" netvision.net.il=""> >Subject: Re: [BioC] problem with hgu133a // GOstats // BioC-R2.1.1 >To: John Zhang <jzhang at="" jimmy.harvard.edu=""> >Cc: bioconductor at stat.math.ethz.ch >MIME-version: 1.0 >Content-transfer-encoding: 7BIT >X-Accept-Language: en-us, en >User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.7.5) Gecko/20041217 >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu >X-Spam-Level: >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham version=3.0.1 > >John Zhang wrote: >> We rely on NCBI for annnotation. 213268_at is annotated to Z98884 by Affymetrix >> and UniGene says it is PER3. >> > >Why do you rely on Unigene, and not on Entrez Gene? > From what I've seen, Unigene tends to unify different Gene settings, >even when the connection between them is unclear (to my examination of >the data). We rely on NCBI as previously mentioned. Data from both Entrez Gene and UniGene were used to obtain unified annotations. e. g. Z98884 is annotated to PER3 by both Entrez Gene and UniGene and that is why that symbol is assigned to the probe. > >Yours, > >Uri David Akavia Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Hi Katleen, For question 1, try on www.bioconductor.org. Also, try the new "biocLite" script that automagically finds most packages. http://www.bioconductor.org/ -> Install How To For question 2, we all know that genome annotations, Unigene etc. change over time, and the three different responses you get seem to reflect that. Have a look at the package documentation of hgu133a, i.e. type: "? hgu133a" for details. In particular the data in the hgu133a package is based on EntrezGene, which might explain the discrepancy with Ensembl. The people that build these packages simply take what the public genome databases provide, we have no resources for correcting their mistakes or in fact for any kind of manual curation. Still, it is of course annoying if you care especially for that gene - in that case there is no other way than curating (that part of) the metadata yourself, perhaps using the AnnBuilder package, or the biomaRt package. For question 3, I pass (don't use MS-Window), but the above-mentioned script biocLite might do. Cheers Wolfgang > > *question 1: GOstats* > When I try to use library(GOstats) in R2.1.1 (with recent installation > of BioC: getBioC()), I get following message: > > Loading required package: graph > Error: package 'graph' could not be loaded > In addition: Warning message: > there is no package called 'graph' in: library(pkg, character.only = > TRUE, logical = TRUE, lib.loc = lib.loc) > > Where can I find the graph package (I haven't found it on the CRAN website)? > > *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 = > */CAMTA1/*. > > 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" > [[1]] > 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, > Katleen > -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber