[BioC] Memory Requirments

Michael Barnes Michael.Barnes at cchmc.org
Wed Jun 25 09:56:12 MEST 2003


What are the memory requirments when running Bioconductor's Affy
package?  I have 38 U95a chips and when I try to process the data I
get:

 expresso(Data,widget=TRUE)
background correction: rma 
normalization: quantiles 
PM/MM correction : pmonly 
expression values: medianpolish 
background correcting...Error: cannot allocate vector of size 83200 Kb
In addition: Warning message: 
Reached total allocation of 1024Mb: see help(memory.size) 

Is this saying that the vector size for each chip is 83Mb?  Otherwise,
what is going on?

In addition, is this a reasonable analysis or is this duplicating the
functions used in rma as may be suggested in "Textual description of
Affy", pg 14?  I don't quite understand from the vignette.

Michael Barnes



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