[BioC] HuGene annotation and htmls

[cstrato]

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", 
varlist="fUnitName:fSymbol:fChromosome:fStart:fStop:fLevel", 
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 
"phenoData".

Best regards
Christian


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
>
>
>
>
>
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