[Bioc-devel] Memory problem in affy package of BioC 1.7 and BioC 1.8

[Seth Falcon]

Hi Mirjam,

Mirjam van Vroonhoven <m.vroonhoven at erasmusmc.nl> writes:
> We have an SGI Origin computation server (32 cpu, 64 Gb RAM) running irix
> 6.5.27. 

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
breath :-)

> 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
> 			ReadAffy()	
> 			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.

Best,

+ seth