[BioC] Gene filtering

[Adaikalavan Ramasamy]

I think justRMA() uses nearly all the memory you have access to, so it
it only able to handle small computations afterwards. What I would
suggest is try saving the exprSet and exit. Then start from a fresh R
session and do your analysis from that. See below.

On Fri, 2005-02-11 at 10:06 +0100, Heike Pospisil wrote:
> 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

To save the object and exit without saving workspace image, type in

	save(data, file="mydata.rda", compress=TRUE)
	quit("no")        


Start R and type in
	load("mydata.rda")
and proceed with your analysis.


> 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
>