[BioC] Memory Issue under WinXP x64 (64 bit Windows XP)

[Carleton Garrett]

Hi

I'm currently running Bioconductor version 2.2.0 under Windows XP x64 
with 16 Gb RAM and Virtual Memory upto 100 Gb.

In trying to combine 67 Affy u133a and 67 Affy u133a_2 cel files I am 
able to form the initial affy batches using read.affybatch() but get a 
memory allocation error (below) when I try to combine them with the 
'combineAffyBatch()' function

Error: cannot allocate vector of size 280,470 Kb

Attempts to increase memory size within 'R' are only partly successful.  
Attempting to increase the memory to 16 Gb (16000 Mb) through using the 
following command

memory.limit(size=16000)

produces the error

Error in memory.size(size) : don't be silly! : your machine has a 4 Gb 
limit [not true according to the OS].

Reducing the number of cel files in the two initial affy batches to 16 
each (but not 33 each) did allow the combined affy batch to be created 
so the combneAffyBatch() function appears to work on this platform.

Two questions:

1)   Does the binary version 2.2.0 of R for Windows have a built-in 
memory limit of 4 Gb? - and if so, is there a way to circumvent this limit?

2)   Is there anything peculiar about the combineAffyBatch() function 
that makes it use memory inefficiently?

    I raise the above question because even when the number of cel files 
was reduced to 33 u133a and 33 u133a_2 there was a memory allocation 
error when I ran combineAffyBatch() that was the same as with the 67 + 
67 cel files (ie, "Error: cannot allocate vector of size 280,470 Kb") 
and yet the memory.limit() was ~4.2 Gb and the memory.size() was only 
~1.4 Gb in a machine with 16 Gb RAM.

Any suggestions welcomed.

Carl Garrett