[BioC] less memory usage
Rafael A. Irizarry
ririzarr at jhsph.edu
Mon Mar 10 11:49:53 MET 2003
hi!
For those having memory problems with the affy package:
James MacDonald has contributed the function justRMA that computes a
pm-only rma without creating an AffyBatch. It reads in cel files and
returns exprSets. It wil be available in the
next release. However, if you need it now,
it is in the development version. if the devel version
gives you trouble, as a last resort, use the rma package that adds it to
whatever version you have now:
http://www.biostat.jhsph.edu/~ririzarr/affy/index.html
Note1: the "official" code for RMA is still in the affy rma funciton but
if this can't handle your large data-set try justRMA.
Note2: you dont need to use ReadAffy. a typical call may be
library(affy)
eset <- justRMA(widget=TRUE) ##or if you dont choose cel files: justRMA()
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