[BioC] Affy EXON Array: iterPLIER or RMA

James W. MacDonald jmacdon at med.umich.edu
Fri May 4 19:14:56 CEST 2007

Crispin Miller wrote:
> I'm not sure if this is your experience too?: we found we need a big
> machine mainly for the normalization/expression summary side of things -
> I don't think the package itself should need too much clout to manage
> the annotation; it's the arrays themselves that eat up the RAM.

Exactly. Well, the cdf package is pretty big as well, although I don't 
know offhand how much RAM it takes. But you are exactly right - the 
arrays are the big RAM users here.

There are two possible fixes in the pipeline. For the cdf there will 
soon be the ability to create a hybrid cdf/annotation package based on a 
SQLite database that will use much less RAM. Because SQLite doesn't have 
the capabilities that MySQL does (stored procedures, for instance), I 
don't think this will be able to supercede exonmap. Rather just 
complement it.

On the array side, there is the BufferedMatrix package which puts most 
of the data on disk (and buffers a small, user adjustable amount of data 
in RAM). The oligo package already uses BufferedMatrix for the raw data 
and I imagine could also use BufferedMatrix for ExpressionSets as well.

So hopefully we will soon get the analysis of these data back onto more 
modest computers.



> Cheers,
> Crispin
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