[BioC] GOLOCUSID and GOALLLOCUSID disagree with AmiGO

[Dick Beyer]

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.

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.

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