On Dec 8, 2007 1:00 AM, Loren Engrav <engrav@u.washington.edu> wrote:

> Ok
> SessionInfo now returns
>
> > sessionInfo()
> R version 2.6.1 (2007-11-26)
> powerpc-apple-darwin8.10.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
> Biobase_1.16.1
>
> But I still get
> > Gibran70 <- ReadAffy()
> Error: cannot allocate vector of size 723.6 Mb
> Although not big red messages which is not quite so hostile
>
> I guess time to go to bed and in the AM buy some RAM
>
> Thank you so much for the help
>
> Engrav
>
>
> > From: Benilton Carvalho <bcarvalh@jhsph.edu>
> > Date: Sat, 8 Dec 2007 00:23:10 -0500
> > To: Loren Engrav <engrav@u.washington.edu>
> > Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
> > Subject: Re: [BioC] Wow, what have I done
> >
> > In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched
> > in terms of memory management, you might want to define beforehand
> > what you're going to be doing and, probably, use functions like
> > justRMA().
>


Hi, Loren.  I would really consider following the advice that Benilton gave
you and use justRMA().  The reason justRMA() was created in the first place
was to solve the memory problem that you are describing.  I didn't see that
you had tried this yet (but I might be mistaken), so I just wanted to remind
you to try it.  If justRMA() will not work for your particular application
for some reason, it is probably worth outlining for us what you want to do,
as it may not be necessary to load all the arrays at once to accomplish the
task.

In the end, you may want to buy RAM for other reasons, but I think a
solution might have been proposed already for your current problem.

Sean

	[[alternative HTML version deleted]]

