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) 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.

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. > > _______________________________________________ > Bioconductor mailing list > 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