[BioC] Memory Requirments

[James MacDonald]

You are duplicating rma with expresso, so you *may* be able to do the
analysis using rma. I am not sure if the memory requirements are
significantly different.

There are at least two alternatives to what you are doing. First, you
can use justRMA to compute the expression values. If you don't have
enough memory to hold an AffyBatch and an exprSet in memory at once
(which appears to be the case), you will have to remove the AffyBatch
first or you will still run out of memory.

The other alternative is to use the functions that Laurent Gautier
posted to the list about a month ago (affyEnvPtr). They are designed to
minimize the amount of memory used by affy.

Jim



James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Michael Barnes" <Michael.Barnes at cchmc.org> 06/25/03 08:56AM >>>
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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