[BioC] question about ontoCompare() performance change

[Scott Markel]

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