[BioC] Error: cannot allocate vector of size ...

Levi Waldron levi.waldron at utoronto.ca
Fri Jul 21 18:43:51 CEST 2006

I'm not sure if this will help, but this is an exerpt from the affy vignette:

5. Read in the data and create an expression, using RMA for example.
   R> Data <- ReadAffy() ##read data in working directory
   R> eset <- rma(Data)

Depending on the size of your dataset and on the memory available to
your system, you might experience errors like 'Cannot allocate vector
. . . '. An obvious option is to increase the memory available to your
R process (by adding memory and/or closing external applications2 . An
another option is to use the function justRMA.

R> eset <- justRMA()

This reads the data and performs the 'RMA' way to preprocess them at
the C level.
One does not need to call ReadAffy, probe level data is never stored
in an AffyBatch.  rma continues to be the recommended function for
computing RMA.

More information about the Bioconductor mailing list