[BioC] Memory problems analyzing 16 chips using arrayQualityMetrics package

Sean Davis sdavis2 at mail.nih.gov
Tue Jul 15 19:53:12 CEST 2008

On Tue, Jul 15, 2008 at 1:34 PM, simona dalle carbonare
<simona.dallecarbonare at gmail.com> wrote:
> Hi,
> I tried to create using the arrayQualityMetrics package a report on 16 chips
> but my pc (32 bit machine with 2 GB of Ram) reports memory problems. Does
> somebody have an idea of the requirements of a PC able to analyze such a
> number of chips?

Hello, again, Simona.  There are a HUGE number of posts in the
bioconductor archives regarding memory issues and affymetrix arrays.
You could certainly search the archives for more information.
However, by using the aroma.affymetrix package or using justRMA and
justGCRMA, you should be able to process that number of arrays on a
modest PC.  As for quality control, you can typically do that in
smaller batches if necessary, as many of the affy quality metrics are
calculated on a per-chip basis.


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