I'm seeing a noticeable performance change in goTools' ontoCompare() from BioConductor version 2.3 to 2.4. With the same input data the user time reported by system.time() on my Windows XP machine has gone from 25 seconds to about 150 seconds. Times on a RHEL 5 machine are 30 seconds and 130 seconds. I checked the ontoCompare() help, the goTools documentation, the mailing list archives, and Google for terms like "ontoCompare goTools performance", and didn't find anything. I'm sure I'm missing something obvious, but I'd appreciate advice on how I should now be using ontoCompare() in Bioc 2.4. The script, BioC 2.3 output, BioC 2.4 output, and two sets of sessionInfo() follow. Scott ############################## Here's the R script, using the same inputs for both BioC 2.3 and 2.4. prop<-list() prop$probeIDs <- c("1007_s_at", "1053_at", "117_at", "121_at", "1255_g_at", "1294_at", "1316_at", "1320_at", "1405_i_at", "1405_i_at") prop$microarrayType <- "hgu133a" library("goTools") library("hgu133a.db") system.time(result <- ontoCompare( list(prop$probeIDs), probeType=as.character(prop$microarrayType), method="none", goType="MF")) ############################## The BioC 2.3 output is user system elapsed 23.31 0.22 25.70 > result binding catalytic activity chemoattractant activity enzyme regulator activity 1 10 4 2 1 molecular transducer activity structural molecule activity 1 5 1 transcription regulator activity NotFound 1 2 0 ############################## The BioC 2.4 output is user system elapsed 151.16 0.41 169.11 > result [,1] catalytic activity 4 binding 10 enzyme regulator activity 1 transcription regulator activity 2 chemoattractant activity 2 molecular transducer activity 5 ############################## > sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133a_2.2.0 hgu133a.db_2.2.0 goTools_1.12.0 [4] GO_2.2.0 annotate_1.18.0 xtable_1.5-4 [7] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 [10] Biobase_2.0.1 ############################## > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a.db_2.2.11 goTools_1.18.0 GO.db_2.2.11 [4] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.6.0 [7] Biobase_2.4.1 ############################## Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel at accelrys.com Accelrys (SciTegic R&D) mobile: +1 858 205 3653 10188 Telesis Court, Suite 100 voice: +1 858 799 5603 San Diego, CA 92121 fax: +1 858 799 5222 USA web: http://www.accelrys.com http://www.linkedin.com/in/smarkel Vice President, Board of Directors: International Society for Computational Biology Co-chair: ISCB Publications Committee Associate Editor: PLoS Computational Biology Editorial Board: Briefings in Bioinformatics

Hello, I have the same problem as Scott. When I compared 2 lists of go term (1000 values for the first list and 4000 for the second list) with the version 1.10 of gotools, the time to make the process was ~10min. Now I must wait several hours to compare the same list. I often stop the process before the end. I try to modify the format of the list that I set in entry, but the result is the same. I also make the same analysis that was given in example in the documentation and the time of the process is ~ 1h30 instead of 5min. While waiting for a solution. Thanks Jean-Pierre PS: Sorry for my english.