Hi Antje, Please don't take conversations off-list. On 4/2/2013 9:27 AM, Antje Kammermeier wrote: > Dear James, > > thank you for your answer. > > I successfully installed 'ragene10sttranscriptcluster.db'. > Unfortunately the error term "getAnnMap: package ragene10stv1 not > available" stayed after the R commans > celfiles.filt<- nsFilter(Celfiles.norm,require.entrez=TRUE, var.cutoff > =0.5)$eset If you re-read what I sent below, you will notice that you need to do two things, one of which you have neglected to do. Best, Jim > > > 2013/4/2 James W. MacDonald <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">> > > Hi Antje, > > > On 4/2/2013 4:07 AM, Antje Kammermeier [guest] wrote: > > Dear team, > > my name is Antje and I am nwe to Bioconductor. Hope all the > description is ok for you. > I analyse Rat Affymetrix data from Rat Gene ST 0.1 Data. I did > a normalisation and wanted to filter the data. I did all the > Installation for the Annotation data. Unfortunately I got the > error term ragene10stv1 not available. Can anybody what can be > wrong? > > > Thanks in foward > > > Antje > > -- output of sessionInfo(): > > R command > celfiles<-ReadAffy() > Celfiles.norm<-rma(celfiles) > > > These arrays can be summarized at two different levels; at the > probeset (roughly exon) and transcript level. Well, not with the > affy package, but with ST-aware packages like oligo, xps, etc. > Because of this, there are two annotation packages for each array, > and you have to specify which one you are using. > > Since you are using affy here, the summarization is at the > transcript level, so you want to do > > annotation(Celfiles.norm) <- "ragene10sttranscriptcluster.db" > > and ensure that you have this package installed, and everything > should proceed normally from here on out. > > Best, > > Jim > > > celfiles.filt<- nsFilter(Celfiles.norm,require.entrez=TRUE, > var.cutoff =0.5)$eset > > Annotation packages installed > AnnotationDbi > pd.ragene.1.0.st.v1 > ragene10stv1cdf > ragene10stv1probe > > > -- > Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org="">. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099