[BioC] Error in processing 47 cel files using expresso.

[Wolfgang Huber]

Anjan

you can either use a computer with more memory or use one of the several 
alternatives to 'expresso' that are more memory-efficient and have been 
discussed on this list so many times already (e.g. affy:rma or the xps 
package).

	Best wishes
	Wolfgang


Il Oct/7/10 6:32 PM, ANJAN PURKAYASTHA ha scritto:
> Hi,
> I'm trying to summarize the results of 47 cel files with the following
> command:
> allMtb.eset.liwong<- expresso(allMtb, normalize.method= "invariantset",
> bg.correct= FALSE, pmcorrect.method= "pmonly", summary.method= "liwong")
> Here is the progress report:
> normalization: invariantset
> PM/MM correction : pmonly
> expression values: liwong
> normalizing...Error: cannot allocate vector of size 360.0 Mb
>
> My sessionInfo:
> R version 2.11.1 (2010-05-31)
> i386-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mouse4302cdf_2.6.0 affy_1.26.1        Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.11.1
>
> Any thoughts on how I can get around the error?
> Thanks,
> Anjan
>