[BioC] HuGene annotation and htmls

cstrato cstrato at aon.at
Thu Apr 9 23:21:39 CEST 2009

Dear Mayte

I am not sure if you can use "hugene10st.db" to get the annotation for 
the results obtained with xps, but maybe I am wrong.

However, you can export your normalized data together with the 
corresponding annotation by simply doing:
 > export(data.rma, treetype="mdp", outfile="Results_mdp.txt")

If you only want to export a subset of variables and also keep the 
result as dataframe you can do:
 > ds <- export(data.rma, treetype="mdp", 
outfile="Result_mdp.txt", as.dataframe=TRUE)
 > head(ds)

You should still be able to convert the expression part from "ds" into 
an ExpressionSet, and probably use the annotation part of "ds" as slot 

Best regards

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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