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" ##############