I ran an analysis analyses using limma on some Affy HuGene 1.0 ST arrays
(i.e. "HuGene-1_0-st-v1" in the @cdfName slot of the affybatch). I want to
output gene symbols with topTable, and I'm trying to follow these
instructions using the annotate package:
https://stat.ethz.ch/pipermail/bioconductor/2009-October/029908.html

I loaded the environments hugene10stv1cdf and hugene10stprobeset.db from
http://www.bioconductor.org/packages/release/data/annotation/

If "probeids" is the ID column from the topTable output, when I try getting
to the gene symbols using getSYMBOL(probeids, "hugene10stprobeset.db"),
every probe ID comes back NA. When I try using getSYMBOL(probeids,
"hugene10stv1cdf"), I get a nasty error:

Error in mget(x, envir = getAnnMap(what, chip = data, load = load),
ifnotfound = NA) :
  error in evaluating the argument 'envir' in selecting a method for
function 'mget': Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
  object 'hugene10stv1cdfSYMBOL' not found

I realize that I could probably use biomaRt to annotate my results, but I
was hoping to do this quickly using one of the annotation files.

How would I most easily output toptable results with gene names (GO terms,
gene descriptions, etc) attached?

Thanks,

Stephen

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