[BioC] Manual annotation of ExpressionSet object created from scratch

Marc Carlson mcarlson at fhcrc.org
Wed Oct 15 18:03:39 CEST 2008

> For building annotation packages, see the AnnotationDbi package and
> the SQLForge vignette.  See the Vignettes in Biobase for discussion of
> AnnotatedDataFrame.  In short, though, an ExpressionSet contains two
> AnnotatedDataFrames, one for the sample information (the phenoData)
> and the other for the features on the array (the featureData).  The
> featureData slot is often redundant if you build an annotation data
> package.  However, you could use it to store a data frame of data from
> ensembl if you like.
> Sean
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Hi Michael,

If you really want to make an annotation package where ensembl IDs are
the main IDs to everything, then you are going to have to first make a
mapping of the ensembl IDs to entrez gene IDs.  This information is
available for a lot of species already and so it can probably be found
in the organism package that matches the critter you are working on
(org.Hs.eg.db for human).  Then you could use that mapping to make a
custom annotation package where the ensembl IDs are basically presented
as if they were the "probes".  But the mappings in that case should be ok.

However, I think its worth noting that unless you have a more complete
ensembl to entrez ID mapping from another source, this is all just
represents a reprocessing of the existing data that can already be found
in the mapping of the appropriate organism package.


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