Entering edit mode
david neil hayes
▴
70
@david-neil-hayes-573
Last seen 10.3 years ago
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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