[BioC] HuGene transcript expression workflow -

[Bruce.Tabor at csiro.au]

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