[BioC] HuGene annotation and htmls

Marc Carlson mcarlson at fhcrc.org
Thu Apr 9 23:26:24 CEST 2009

Hi Mayte,

I can't tell from your post what you tried to do, or even what exactly
you need to know.  Please give us the code you were trying to use, along
with an example that didn't behave the way you expected it to and you
the results of calling sessionInfo() after you did that. You can find
other helpful tips on the posting guide:


What little I can discern from your post I will try to answer.  To use
getSYMBOL() or lookUp(), you need to 1st of all make sure that you have
loaded the annotate package.  Then you need to call it correctly.  Here
is an example that I did using the very latest version of the
hugene10st.db package.

keys = c("7903193","7903204")

getSYMBOL(keys, "hugene10st")

lookUp(keys, "hugene10st" , "CHR")
lookUp(keys, "hugene10st" , "ENTREZID")

Hope this helps,


Mayte Suarez-Farinas wrote:
> I am learning to work with the HuGene ST1 chips.
> I was able to use xps to read and preprocess the files
> and then I convert to ExpressionSet class to use limma
> for modelling.
> Next step I stop: the annotation.
> I load  library("hugene10st.db") but the normal functions
> to create html annotation does not seems to work on this chip.
> I also try to get each component using getSYMBOL and lookUP
> with no success.
> what's the way to go???
> Thanks
> Mayte
> 	[[alternative HTML version deleted]]
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