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

[Levi Waldron]

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.