[BioC] memory - global test

[Simo.rossi]

Hi Seth, thank you in advance!

 I have 1.5 Gb RAM on my PC.

 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.

 Thanks, Simona
>
>
>>
>> I suspect you simply do not have enought RAM to run 280 samples on
>> your machine. Do you want to give us sessionInfo() output and details
>> about your system such as how much RAM is there?
>>
>> Note also that it will help if you give us some context and
>> description of the operations you are attempting.
>>
>> + seth
>> 




--------- Original Message --------
	




Da: Seth Falcon <sfalcon at fhcrc.org>
	To: 
	        Cc: bioconductor at stat.math.ethz.ch
	Oggetto: Re: [BioC] memory - global test
	Data: 30/07/07 16:41
	
	> 
> 
> 
> "Simo.rossi" <simo.rossi at email.it> writes:
> 
> > Hi,
> >
> > I get an error saying " Cannot allocate vector of size 95Mb", using
'Global
> > test' function.
> > I used as input a matrix, not an Expression Set, I have to use it to
limit
> > memory? Or it is not important?
> >
> > My datasets contains 280 samples and 22215 probes: It's a problem?
> >
> > I increased memory size.
> 
> I suspect you simply do not have enought RAM to run 280 samples on
> your machine.  Do you want to give us sessionInfo() output and details
> about your system such as how much RAM is there?
> 
> Note also that it will help if you give us some context and
> description of the operations you are attempting.
> 
> + seth
> 
> -- 
> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
Center
> BioC: http://bioconductor.org/
> Blog: http://userprimary.net/user/
> 
> 
>  
 --
 Email.it, the professional e-mail, gratis per te: http://www.email.it/f
 
 Sponsor:
 In REGALO 'Meravigliosa Creatura' la super hit di GIANNA NANNINI
 Clicca qui: http://adv.email.it/cgi-bin/foclick.cgi?mid=6615&d=20070730