[BioC] affy & problems with not enough avaliable memory

[Ettinger, Nicholas]

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)