[BioC] out of memory problem using affycoretools

Jenny Drnevich drnevich at uiuc.edu
Thu Dec 7 17:07:44 CET 2006

Hi James,

See 'justRMA' - this was developed to help with the memory limitation 
issues. You really should give the codes you used that led to the error 
message, plus the output of 'sessionInfo()' for us to be able to help you 
better. For example, the output of 'rma' should only give one value per 
probeSET, which is composed of 11 probes, in Affy terminology. That you 
said you are getting 11 lines for each "individual probe" (probeset, I 
assume?) means that you were not calling the right function. What was the 
code you used that supposed led to 11 values after 'rma'?


At 08:55 AM 12/7/2006, James Anderson wrote:
>   I have about 53 cel files, each one has the size of about 12-13 mega 
> bytes with 22625 probes. I am using affycoretools to do rma, but it 
> complains that the maximum size of memory has been reached. My PC is 
> Windows XP with 2G RAM. Below is the error information.
>Error: cannot allocate vector of size 209906 Kb
>In addition: Warning messages:
>1: Incompatible phenoData object. Created a new one.
>  in: read.affybatch(filenames = filenames, phenoData = phenoData)
>2: Reached total allocation of 1024Mb: see help(memory.size)
>3: Reached total allocation of 1024Mb: see help(memory.size)
>Since RMA is an across sample normalization, and I need to analyze all the 
>53 samples together, I can not separate them into several pieces and then 
>do RMA, MAS5 can do that, but the expression value obtained by MAS5 is not 
>as good as that of RMA. Does anybody know how to solve this problem? In 
>addition, it seems that the output of rma in affy package (not 
>affycoretools) has several lines for each individual probe (my case is 11 
>lines for each individual probe), while the rma in affycoretools directly 
>gives the final expression value for each probe, could anybody tell me how 
>to make the two results from affy and affycoretools comparable with each 
>Thanks a lot!
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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