[BioC] Gene filtering

[Heike Pospisil]

Dear list members,

I have a very naiv question and I think it is really simple - but I 
didn't solve the problem :-(

I have 79 Affymetrix chips and performed justRMA() first.

 >data
Expression Set (exprSet) with
        54675 genes
        79 samples
                 phenoData object with 3 variables and 79 cases
         varLabels
                cyto: read from file
                vivo: read from file
                vitro: read from file

Now, I want to filter out those genes showing no significant expression 
change (decrease or increase). I used  the genefilter function:

ff1<-ttest(data.frame(data),.001,na.rm=TRUE)
ff2<-filterfun(ff1)
wh2<-genefilter(exprs(eset), ff2)

Unfortunately, I've got the following message: "Error: cannot allocate 
vector of size 168723 Kb"

Do I have a chance to filter out my genes that way? Or is it necessary 
to split the expression set? Any hint?

Thanks a lot in advance,
Heike

-- 
Dr. Heike Pospisil
Center for Bioinformatics, University of Hamburg
Bundesstrasse 43, 20146 Hamburg, Germany
phone: +49-40-42838-7303 fax: +49-40-42838-7312