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

Tae-Hoon Chung thchung at tgen.org
Wed Jun 30 20:30:01 CEST 2004

Right now, I am using Mac OS X 10.3.3 with 1.5 GB memory.
I recently performed data preprocessing of HG_U133 Version 2.
I was able to do RMA analysis up to 100 CEL files successfully.
However, I was not able to do it for 150 CEL files, unfortunately. -_-;;
(I think the job crashed around 130 CEL files, but I am not sure ...)
If your machine has 1GB memory, I think the limit of CEL files you can 
do analysis must be around 60 or 70.
Good luck!

On Jun 29, 2004, at 2:53 PM, Li, Aiguo (NIH/NCI) wrote:

> 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 in
> text format is about 32MB.  Currently we have more than 100 chips and 
> number
> 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 
> "expresso(d,
> normalize.method ="invariantset", bg.correct = FALSE,
> pmcorrect.method="pmonly", summary.method="liwong"" and it ran out of 
> memory
> before the completion.  I have option to upgrade my memory to 4GB, but 
> still
> concern whether it will really help when our chips number reaches 
> several
> hundres or thousands.
> Does anybody can help me with some suggestions?
> Thanks in advance.
> 	[[alternative HTML version deleted]]
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Tae-Hoon Chung, Ph.D

Post-doctoral Research Fellow
Molecular Diagnostics and Target Validation Division
Translational Genomics Research Institute
1275 W Washington St, Tempe AZ 85281 USA
Phone: 602-343-8724

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