[BioC] marrayNorm to exprSet object

Daniel Brewer daniel.brewer at icr.ac.uk
Fri Jul 7 14:20:17 CEST 2006

> Hi, Daniel.  Welcome to bioconductor.
> The geneNames slot of an exprSet is meant to hold the unique name for
> each feature on the array, like the affy probeset id, for example.  It
> can hold the actual names of genes, but then will probably not be
> unique.  In the larger picture, the exprSet is not meant to hold any
> annotation at all.  It was designed to be used in conjunction with a
> bioconductor annotation package.  I personally find exprSets a bit
> difficult to use when I am using my own annotation, just for this
> reason.  What array platform are you using and what are you trying to
> accomplish with converting to an exprSet?
> Sean

I am using custom made cDNA arrays (and later on BACs etc. but always
two colour arrays).  The current approach that I am using is
genepix->marray->exprSet. From there I am interested in doing quite a
bit of analysis including differential analysis, clustering etc. and
then when I have interesting lists go down the annotation path.  I would
like the cloneIDs (unique identifyer) to be always associated with the
current working object, which does not seem to be the case at the moment.

I was under the impression that the way that bioconductor worked, was to
use one of a number of approaches to get to the an exprSet object and
then use that object to do all the analysis.  Please correct me if I am

Thanks again


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