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Dick Beyer
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@dick-beyer-26
Last seen 10.2 years ago
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