[BioC] HuGene transcript expression workflow -
bcarvalh at jhsph.edu
Fri Dec 18 03:35:08 CET 2009
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.
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:
> 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
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor