Entering edit mode
Just a quick FYI to anyone else using goTools' ontoCompare().
It looks like it's approximately another factor of 2 slower in
BioConductor 2.5. User time has gone from 25 seconds (2.3) to
150 seconds (2.4) to 290 seconds (2.5). Don't know if this is
package-specific or caused by changes in R.
Scott
-----Original Message-----
From: Scott Markel
Sent: Wednesday, 10 June 2009 5:15 PM
To: Bioconductor at stat.math.ethz.ch
Subject: question about ontoCompare() performance change
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
