[BioC] Many missing GO terms from GOHyperG call using mgu74av2

[Dick Beyer]

In the course of using GOHyperG, I checked my results against results from NETAFFX and found large discrepancies in the number of GO terms returned for some probeids.

Here is an example code snippet that illustrates my point:

library(affy)
library(mgu74av2)
library(GOstats)
library(annaffy)
smallList <- c("160102_at")
myLL <- unlist(mget(smallList, mgu74av2LOCUSID))
sum(duplicated(myLL))
length(myLLunique<- !duplicated(mget(smallList, mgu74av2LOCUSID)))
bphyper <- GOHyperG(myLL[myLLunique], lib="mgu74av2", what="BP")

sort(names(bphyper$go2Affy))
[1] "GO:0006457" "GO:0007582" "GO:0008150" "GO:0008152" "GO:0009987" "GO:0019538"
[7] "GO:0043170" "GO:0050875"

#From NETAFFX for 160102_at
#"GO:0006457" "GO:0007582" "GO:0008150" "GO:0008152" "GO:0009987" "GO:0019538"
#"GO:0043170" "GO:0050875"
#"GO:0044238" "GO:0044237" "GO:0044260" "GO:0044260" "GO:0044267

Notice that NETAFFX returns 5 additional GO terms that are missing from the results from the GOHyperG call.

Here is my sessionInfo:

> sessionInfo()
R version 2.1.0, 2005-04-18, i386-pc-mingw32

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics" 
[6] "grDevices" "utils"     "datasets"  "base"

other attached packages:
    annaffy       KEGG   hgu95av2    GOstats   multtest genefilter
   "1.0.18"    "1.6.8"    "1.8.4"    "1.1.2"    "1.6.0"    "1.6.1"
   survival     xtable       RBGL   annotate         GO        XML
     "2.17"    "1.2-5"    "1.3.7"   "1.5.15"    "1.6.8"   "0.95-6"
      graph      Ruuid    cluster   mgu74av2       affy reposTools
    "1.5.0"    "1.5.0"    "1.9.8"    "1.8.4"    "1.6.7"   "1.5.19"
    Biobase
   "1.5.12"

Is this a problem with the mgu74av2 metadata, or with GOHyperG?

Thanks much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer