[BioC] Memory Problems

[david neil hayes]

Thanks to Dr. Huber for the response to my earlier question.  Another 
matchprobes question that may have more general interest in terms of memory 
usage (which in my experience has been a bigger problem than processing 
speed)

I have a folder of files, each file representing one affybatch object (which 
is a single array).  I am using the "load" command to read these files in 
batches of 10, then I perform a "combine" function.   I save the results to 
a file, then move on to the next batch of 10.

I find that my page file usage continues to increase, even though I have 
"removed" the original 10 affybatch objects and all references to them.  As 
you might expect, I quickly exhaust my RAM.  I have been unable to solve 
this on my own.  In talking with some of the Bioconductor staff, I 
understand this may relate to the environments used in the affy package.

To reduce my memory usage I have tried:
  affybatch <- 0
  gc()
  rm(affybatch)
  putting the entire batching process in a separate function function from 
which I exit before
     moving to the next batch

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