[BioC] Memory issue on Linux running Affymetrix HG-U133_Plus_2
dgrigor1 at jhmi.edu
Thu Jan 19 17:28:13 CET 2006
I've read here that nobody had a problem running gcRMA on Linux.
Surprisingly I do.
I run 36 HG-U133_Plus_2 cel files using 1G of RAM and 2G of swapping memory
and get this message
Error: cannot allocate vector of size 359894 Kb
Note that regular RMA runs just fine.
Then I read specifications for gcRMA and found recommendation to have 1.25G
So I've upgraded my machine to 1.5G and got exactly the same message
Error: cannot allocate vector of size 359894 Kb.
What else could you recommend to solve the problem?
Is it feasible to split gcRMA runs then combine data in Excel and normalize
it using column average?
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