[BioC] memory - global test

[Seth Falcon]

"Simo.rossi" <simo.rossi at email.it> writes:

> 	
> Hi Seth, thank you in advance!
>
>  I have 1.5 Gb RAM on my PC.

sessionInfo()?  We'll assume Windows.  1.5GB RAM may not be enough to
do the computations you are interested in...

>  I try to elaborate the following operations:
>
>>esetdata <- read.table (file="H_S.txt", sep="\t",header=TRUE,row.names=1 )
>
>>x<-as.matrix(esetdata);
>>xnorm<-normalize.quantiles(x)
>>go <- as.list(hgu133aGO2ALLPROBES);
>>go <- lapply(go, function(x) x[!is.na(names(x)) & (names(x) !="IEA")]);
>>GO.cellcycle <- go[["GO:0016520"]]
>>gt<-globaltest(xnorm, y, GO.cellcycle);
>>sampled.gt <- sampling(gt)
>
>  I'm not able to performe global test for 281 samples, It is ok for 171
>  samples.

You might be able to handle a few more arrays if after creating xnorm,
y, and GO.cellcycle, you save these variables to disk using save(),
restart R and then load them up again.


+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/