[BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO

[John Zhang]

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