[BioC] affy & problems with not enough avaliable memory

Benjamin Otto b.otto at uke.uni-hamburg.de
Tue Jan 17 10:58:44 CET 2006

Hi Nick,

is this a new call or did I just recieve some delated second copy of your
first Thread? If it is indeed a new mail, could you maybe summarize which of
the previous suggestions worked with you and which not? Do you still have
the problems with GCRMA or is it still MAS5 and LiWong? In addition:

* What does the command "memory.limit()" spit out after increasing the max
memory size to 2000kb?
* Did you try justRMA, justGCRMA and justMas()?


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Ettinger,
> Nicholas
> Sent: 15 January 2006 20:47
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] affy & problems with not enough avaliable memory
> Hello all!
> I have 16 Affy Hg-U133-plus-2 CEL files that I am trying to analyze.  I
> am having difficulties generating expression data because of memory
> problems.  I am working on a Dell desktop running WinXP.  I can generate
> expression values if I use "RMA" but if I try MAS5 or GCRMA or LiWong
> instead then I consistently get an error message with "Cannot allocate
> vector of size 169362 Kb."  To try to increase available memory I have
> already done two things:  (a) I right-clicked on the R icon and changed
> the slot marked 'Target' to read ""C:\Program
> Files\R\R-2.2.0\bin\Rgui.exe" --sdi  --max-mem-size=2000M" and (b) I
> have changed the virtual memory so that the Total Paging File size is
> 2000MB.
> Despite these efforts, I still get problems with not enough memory.
> What can I do?  Do I have to normalize all 16 arrays at once?  Is it
> still valid to do them piecemeal?  My gut says no.  This is getting
> frustrating.....i don't really have access to a bigger computer that I
> know of.
> Suggestions would be very, very welcome!!!
> Thank you.
> ---Nick
> library(webbioc)	##load the relevant packages
> library(siggenes)
> library(hgu133plus2)
> library(annotate)
> TotalData <- ReadAffy()
> eset_mas5 <- mas5(TotalData)
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