[BioC] A question related to handling large data analysis inbioconducto r

James MacDonald jmacdon at med.umich.edu
Wed Jun 30 18:08:42 CEST 2004

If you are planning on using that number of chips, at the moment the
only recourse is to use a 64 bit architecture which will allow you to
use more than 4 Gb RAM. Even using justRMA I bet you will not be able to
do more than 50 - 60 of the version 2 chips with only 1 Gb RAM.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> "Li, Aiguo (NIH/NCI)" <liai at mail.nih.gov> 06/29/04 5:53 PM >>>
Hi all.
My name is AG LEE, a new bioconductor user. Our project is using HG_U133
plus 2 chips which contain approximately 56,000 probes and the .cel file
text format is about 32MB.  Currently we have more than 100 chips and
is growing quickly.  I tried to get the data into bioconductor using
ReadAffy and can only read in 19 chips before it run out of memory (my
machine has 1 GB memory).  I tried to normalize the data using
normalize.method ="invariantset", bg.correct = FALSE,
pmcorrect.method="pmonly", summary.method="liwong"" and it ran out of
before the completion.  I have option to upgrade my memory to 4GB, but
concern whether it will really help when our chips number reaches
hundres or thousands.
Does anybody can help me with some suggestions?
Thanks in advance.

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