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

[Dick Beyer]

Hi John,

Thanks for the good suggestion.  Is there a way to tell what the date of the GO information is used in a particular build of an annotation package?  I'm asking so I can figure out if doing my own build at any particular time is warranted.

Thanks very 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
*******************************************************************************

On Wed, 29 Jun 2005, John Zhang wrote:

>
>> 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
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>