Hi All, I have recently been asked to analyse 27 CEL files from Affymetrix's Human Gene 1.0 ST (HuGene) array. I have processed analysed U133 and HuExon chips before and substantial documentation exists for these chips. However I'm struggling to even find a workflow description for the HuGene chips to go from CEL files to an annotated output. I'm using R-2.8.1 in Linux. The documentation provided with the oligo package seems designed for SNP analysis. I've installed pd.hugene.1.0.st.v1, but this only gives probeset summaries. See: https://stat.ethz.ch/pipermail/bioconductor/2009-July/028893.html I can't install hugene10sttranscriptcluster.db, because I can't install AnnotationDbi-1.7.20 (or above) (Maybe I need R-2.10.1?) Even if I did install hugene10sttranscriptcluster.db I'm not sure how to attach the annotation after a limma analysis. Thanks in advance, Bruce Tabor

Use R-2.10.x, update BioConductor, reinstall de pd.hugene pkg and you'll get summaries at the trascript level using something like: rawData = read.celfiles(list.celfiles()) rmaData = rma(rawData, target="core") then install the transcript package. Cheers, b On Dec 18, 2009, at 12:20 AM, Bruce.Tabor at csiro.au wrote: > Hi All, > > I have recently been asked to analyse 27 CEL files from Affymetrix's Human Gene 1.0 ST (HuGene) array. > > I have processed analysed U133 and HuExon chips before and substantial documentation exists for these chips. > > However I'm struggling to even find a workflow description for the HuGene chips to go from CEL files to an annotated output. > > I'm using R-2.8.1 in Linux. > > The documentation provided with the oligo package seems designed for SNP analysis. > > I've installed pd.hugene.1.0.st.v1, but this only gives probeset summaries. See: > https://stat.ethz.ch/pipermail/bioconductor/2009-July/028893.html > > I can't install hugene10sttranscriptcluster.db, because I can't install AnnotationDbi-1.7.20 (or above) (Maybe I need R-2.10.1?) > > Even if I did install hugene10sttranscriptcluster.db I'm not sure how to attach the annotation after a limma analysis. > > Thanks in advance, > > > Bruce Tabor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor