[BioC] need help regarding quality assessment of raw data

[Steve Lianoglou]

Hi Varshika,

Please CC the bioc-list so that you can get more eyeballs to help w/
your problem, and any help that you do receive will be useful to
others.

so:

On Tue, Jan 8, 2013 at 11:49 AM, varshika singh
<varshika13singh at gmail.com> wrote:
> hi,
> size of arrays=1164x1164 features (13 kb)

You still haven't answered how many arrays you are trying to process.
All signs are pointing to the fact that you do not have enough RAM on
your machine -- even if you did it wouldn't help because you are
running R in 32bit mode.

I'm not sure what other help I can offer other than suggesting you
hunt for a larger (more ram) machine to do the arrayQC and
normalization steps so that you can hopefully continue w/ downstream
analysis on your own machine.

I know the aroma suite of tools can process lots of arrays on low ram
machines, so you can use that to normalize, but I'm not sure what type
of QC reports they generate along the way.

Perhaps others may have more useful suggestions,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact