[Bioc-devel] Memory problem in affy package of BioC 1.7 and BioC 1.8
sfalcon at fhcrc.org
Mon May 15 07:35:45 CEST 2006
Mirjam van Vroonhoven <m.vroonhoven at erasmusmc.nl> writes:
> We have an SGI Origin computation server (32 cpu, 64 Gb RAM) running irix
We don't have such a system which makes reproducing/debugging this
issue rather difficult. If anyone else on the list has such a system,
it would be great to attempt to reproduce this (I'm not holding my
> In the newer versions of R we receive memory errors in the affy library, in the
> ReadAffy() and the mas5() command, and we also saw them in the vsn
> normalization from the vsn library. The same commands run fine in R 2.0.0, on
> the same CEL files. It depends on the set of CEL files used, whether we see
> errors or not, i.e. enlarging or reducing the set of CEL files with one
> or more arrays may introduce the error.
> example output in R 2.2.1:
> And in R 2.3.0 it yields also an error:
> R : Copyright 2006, The R Foundation for Statistical Computing
> Version 2.3.0 (2006-04-24)
> ISBN 3-900051-07-0
> <snipped the default R message>
> > library(affy)
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> Vignettes contain introductory material.
> To view, simply type 'openVignette()' or start with 'help(Biobase)'.
> For details on reading vignettes, see the openVignette help page.
> Loading required package: affyio
> > data<-ReadAffy()
> > data2<-mas5(data)
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...Error: cannot allocate vector of size 188830 Kb
affy and vsn aside, with R 2.3.0 can you address a reasonable amount
of your RAM? For example, you can test by allocating many large
sequence vectors: v <- seq(1, 2^29)
> The memory error occured while 37 Gb of RAM was free.
> Memory usage after in mas5() command
> R 2.0.0 / BioC 1.5 1070M 1189M - 1854M - 2060M
> R 2.2.1 / BioC 1.7 851M 1220M - crash
> R 2.3.0 / BioC 1.8 1058M 1242M - crash
> I'm puzzled by this....
> Has anybody else seen this behaviour?
If you can share your cel files, we could try to reproduce this on a
different system. We have a Linux based system that has a fair amount
of RAM, but not 64GB.
> Is this a bug in the affy package?
Hard to say. You mentioned that you had a similar issue with vsn.
> Is there a place that I can submit bug reports?
This is the place, although it is also recommended to correspond with
package maintainers directly.
Sorry I can't be more helpful.
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