[BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO

[Dick Beyer]

Hi John,

Thanks for looking into this.

The AmiGO build is stated at the AmiGO website is for Jan. 28, 2005.  For GO, it is

      Gene Ontology:<URL:
      http://www.godatabase.org/dev/database/archive/2004-09-01/go_20040
      9-termdb.xml.gz>. Built: 2004-09-01

      LocusLink:<URL:
      ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>. Built:
      January  5, 2005

So there are some differences in the date, but I guess I wouldn't expect such a huge change from 33 genes to 8.

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
*******************************************************************************

On Fri, 28 Jan 2005, John Zhang wrote:

>
>> I am having some trouble understanding the correct usage of GOLOCUSID and
> GOALLLOCUSID.  I can't get the list of LocusLink identifiers output for a
> particular GOID to agree with AmiGO.  Also, for this particular GOID,
> GO:0000158, the return from GOLOCUSID and GOALLLOCUSID are the same, which seems
> wrong.  I am using the latest development version of GO.
>
>
> GO:0000158 does not have any children so that GOLOCUSID and GOALLLOCUSID are the
> same.
>
>
>>
>> Then again, perhaps I am not approaching this correctly as I have not used
> these functions before.
>>
>> AmiGO shows 8 genes for GO:0000158, and both GOLOCUSID and GOALLLOCUSID show
> 33.
>
> Depanding on the buid of the GO package and when you checked the data against
> AmiGO, there may be some differences.
>
> I will look into this next week (have to leave). Thanks.
>
>
>>
>> Would someone please look at the following code example and tell me what I am
> doing wrong?
>>
>>> require("GO") || stop("GO unavailable")
>>> myGOALLLOCUSID  <- as.list(GOALLLOCUSID)
>>> allGOALLLOCUSID <- names(myGOALLLOCUSID)
>>> allGOALLLOCUSID <- sub("GO:","",allGOALLLOCUSID)
>>> myGOLOCUSID     <- as.list(GOLOCUSID)
>>> allGOLOCUSID    <- names(myGOLOCUSID)
>>> allGOLOCUSID    <- sub("GO:","",allGOLOCUSID)
>>> which(allGOLOCUSID == "0000158")
>> [1] 3370
>>> myGOLOCUSID[3370]
>> $"GO:0000158"
>>    IDA    IDA    IEA    IEA    IEA    IEA    IEA    IEA    IEA    IEA    IEA
> IEA    IEA
>>  24673   5520 116663  19053  24666  24668  24669  24672  24673  24674  24675
> 25594  65179
>>    IMP    ISS    ISS    ISS    ISS    ISS    ISS    ISS    ISS    ISS    ISS
> ISS    ISS
>>  45959 117281  19045  19046  19052  19053  19055  28227 319520  39337  45959
> 47877  63953
>>    ISS    NAS     NR     NR    TAS    TAS    TAS
>>  67857  45959   5518   5519  19052  24672   5516
>>
>>> which(allGOALLLOCUSID == "0000158")
>> [1] 2856
>>> myGOALLLOCUSID[2856]
>> $"GO:0000158"
>>    IDA    IDA    IEA    IEA    IEA    IEA    IEA    IEA    IEA    IEA    IEA
> IEA    IEA
>>  24673   5520 116663  19053  24666  24668  24669  24672  24673  24674  24675
> 25594  65179
>>    IMP    ISS    ISS    ISS    ISS    ISS    ISS    ISS    ISS    ISS    ISS
> ISS    ISS
>>  45959 117281  19045  19046  19052  19053  19055  28227 319520  39337  45959
> 47877  63953
>>    ISS    NAS     NR     NR    TAS    TAS    TAS
>>  67857  45959   5518   5519  19052  24672   5516
>>
>>
>>
>> AmiGO tells me GO:0000158 has the genes:
>> 19045	Ppp1ca
>> 19046	Ppp1cb
>> 19052	Ppp2ca
>> 19053	Ppp2cb
>> 19055	Ppp3ca
>> 63953	Dusp10
>> 319520	Dusp4
>> 67857	Ppp6c
>>
>> base 2.0.1
>> datasets 2.0.1
>> utils 2.0.1
>> grDevices 2.0.1
>> graphics 2.0.1
>> stats 2.0.1
>> methods 2.0.1
>> tools 2.0.1
>> Biobase 1.5.0
>> reposTools 1.5.1
>> affy 1.5.8
>> matchprobes 1.0.12
>> gcrma 1.1.1
>> qvalue 1.1
>> siggenes 1.2.11
>> limma 1.8.6
>> GO 1.6.8
>> xtable 1.2-4
>>
>> Thanks very much for any help or suggestions,
>> 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
>>
>> _______________________________________________
>> 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
>
>