[BioC] Very high memory usage using annaffy method aafTableFrame under R 2.4 and above

[Dave Campbell]

Hello;

   We are using bioconductor/R to analyze Affymetrix microarrays.  The 
code is based on the webbioc package, and was written when the current 
version of R was 2.2.x.  We have found that with R versions 2.4.0 and 
above (2.4.1 and 2.5.0 have been tested), one method in the annaffy 
package, aafDataFrame() seems to consume memory until the machine runs 
out and R is aborted (this is the case on a 4 GB and an 8 GB linux 
system).  We use biocLite() to install the bioconductor packages, so I 
believe that they are the appropriate versions.

  The simple script below runs in about 1.5 minutes on 2.2.1 and 2.3.0, 
and consumes around 200 MB of memory.  As stated, on 2.4.1 and 2.5.0 it 
never completes, and has been seen to consume in excess of 4 GB of 
memory.  The output from the run on 2.5.0 is shown at the bottom, this 
includes the bioconductor package versions.

## TEST SCRIPT ##

R.version;

library(tools);
library(Biobase);
library(annaffy);
library(affy);
package.version('affy');
package.version('Biobase');
package.version('tools');
package.version('annaffy');

path.to.annotation <- "/net/arrays/Affymetrix/library_files";
chip.name <- "HG-U133_Plus_2";

annot <- read.csv(paste (path.to.annotation, "/" 
,chip.name,"_annot.csv",sep=""),header=T);
print ( "Annotation file read" );

# Make aaftable object from the annotation data
anno.aaftable      <- aafTableFrame(annot, signed = FALSE);
print( "Done" );

############# 

Thanks for any suggestions you can offer, please let me know if there is 
a more appropriate forum to which to post this inquiry.

-Dave



##  OUTPUT ##

 > R.version;
               _
platform       i686-pc-linux-gnu
arch           i686
os             linux-gnu
system         i686, linux-gnu
status
major          2
minor          5.0
year           2007
month          04
day            23
svn rev        41293
language       R
version.string R version 2.5.0 (2007-04-23)
 >
 > library(tools);
 > library(Biobase);
 > library(annaffy);
 > library(affy);
 > package.version('affy');
[1] "1.14.0"
 > package.version('Biobase');
[1] "1.14.0"
 > package.version('tools');
[1] "2.5.0"
 > package.version('annaffy');
[1] "1.8.1"


[1] "Annotation file read"



##############