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

[John Zhang]

>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.

Unless we build the annotation packages frequently (every week?), there will be 
descripancies. You may try to build your own annotation packages to minimize the 
descripancies.  

>
>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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084