[BioC] HuGene transcript expression workflow -

Benilton Carvalho 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.

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
> 
> 
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