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

[John Zhang]

Yes, ?GO or ?hgu95av2GO ...

>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>Date: Wed, 29 Jun 2005 09:14:25 -0700 (PDT)
>From: Dick Beyer <dbeyer at u.washington.edu>
>To: John Zhang <jzhang at jimmy.harvard.edu>
>Cc: Bioconductor <bioconductor at stat.math.ethz.ch>
>Subject: Re: [BioC] Many missing GO terms from GOHyperG call using mgu74av2
>MIME-Version: 1.0
>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on  
pascal.dfci.harvard.edu
>X-Spam-Level: 
>X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham  
version=3.0.1
>
>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
>>>
>>> _______________________________________________
>>> 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
>>
>>
>

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