[BioC] memory - global test
Seth Falcon
sfalcon at fhcrc.org
Mon Jul 30 17:58:23 CEST 2007
"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/
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