[BioC] Bug in getOntoly-function (package annotate)?
Jukka Hiissa
jahiis at utu.fi
Thu Oct 2 19:41:19 CEST 2008
Hi Marc and thanks for the fast reply.
That is correct, I am using a custom-made annotation package. I have
attached the list returned by the command getGO( "7650504",
"illuminaHumanBCv2")[[1]] at the end of my message.
Here is my sessionInfo:
> sessionInfo()
R version 2.6.1 (2007-11-26)
i486-pc-linux-gnu
locale:
LC_CTYPE
=
en_US
.UTF
-8
;LC_NUMERIC
=
C
;LC_TIME
=
en_US
.UTF
-8
;LC_COLLATE
=
en_US
.UTF
-8
;LC_MONETARY
=
en_US
.UTF
-8
;LC_MESSAGES
=
en_US
.UTF
-8
;LC_PAPER
=
en_US
.UTF
-8
;LC_NAME
=
C
;LC_ADDRESS
=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] illuminaHumanBCv2_08.08.07 annotate_1.18.0
[3] xtable_1.5-2 AnnotationDbi_1.0.6
[5] RSQLite_0.6-7 DBI_0.2-4
[7] Biobase_1.16.2
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
>
I know that my R and BioC are slightly old, but I will upgrade them
(and also my Ubuntu 7.10) as soon as I have finished my current
analysis, hopely within a few weeks. The version of the annotate
package was originally 1.16.1 but I upgraded it manually, just in
case.
By the way, I commented the line "onts = onts[!is.na(onts)]" in the
getOntology-function and now it seems to work.
Best regards,
Jukka
> getGO("7650504", "illuminaHumanBCv2")[[1]]
$`GO:0000159`
$`GO:0000159`$GOID
[1] "GO:0000159"
$`GO:0000159`$Evidence
[1] "TAS"
$`GO:0000159`$Ontology
[1] "CC"
$`GO:0005524`
$`GO:0005524`$GOID
[1] "GO:0005524"
$`GO:0005524`$Evidence
[1] "IDA"
$`GO:0005524`$Ontology
[1] "MF"
$`GO:0005625`
$`GO:0005625`$GOID
[1] "GO:0005625"
$`GO:0005625`$Evidence
[1] "TAS"
$`GO:0005625`$Ontology
[1] "CC"
$`GO:0008160`
$`GO:0008160`$GOID
[1] "GO:0008160"
$`GO:0008160`$Evidence
[1] "IDA"
$`GO:0008160`$Ontology
[1] "MF"
$`GO:0008601`
$`GO:0008601`$GOID
[1] "GO:0008601"
$`GO:0008601`$Evidence
[1] "IDA"
$`GO:0008601`$Ontology
[1] "MF"
$`GO:0008601`
$`GO:0008601`$GOID
[1] "GO:0008601"
$`GO:0008601`$Evidence
[1] "TAS"
$`GO:0008601`$Ontology
[1] "MF"
$`GO:0016887`
$`GO:0016887`$GOID
[1] "GO:0016887"
$`GO:0016887`$Evidence
[1] "IDA"
$`GO:0016887`$Ontology
[1] "MF"
$`GO:0019211`
$`GO:0019211`$GOID
[1] "GO:0019211"
$`GO:0019211`$Evidence
[1] "IEA"
$`GO:0019211`$Ontology
[1] "MF"
$`GO:0032515`
$`GO:0032515`$GOID
[1] "GO:0032515"
$`GO:0032515`$Evidence
[1] "IDA"
$`GO:0032515`$Ontology
[1] NA
$`GO:0032516`
$`GO:0032516`$GOID
[1] "GO:0032516"
$`GO:0032516`$Evidence
[1] "IDA"
$`GO:0032516`$Ontology
[1] NA
$`GO:0035307`
$`GO:0035307`$GOID
[1] "GO:0035307"
$`GO:0035307`$Evidence
[1] "IDA"
$`GO:0035307`$Ontology
[1] "BP"
$`GO:0035308`
$`GO:0035308`$GOID
[1] "GO:0035308"
$`GO:0035308`$Evidence
[1] "IDA"
$`GO:0035308`$Ontology
[1] "BP"
$`GO:0042803`
$`GO:0042803`$GOID
[1] "GO:0042803"
$`GO:0042803`$Evidence
[1] "IDA"
$`GO:0042803`$Ontology
[1] "MF"
$`GO:0046982`
$`GO:0046982`$GOID
[1] "GO:0046982"
$`GO:0046982`$Evidence
[1] "TAS"
$`GO:0046982`$Ontology
[1] "MF"
$`GO:0051721`
$`GO:0051721`$GOID
[1] "GO:0051721"
$`GO:0051721`$Evidence
[1] "IDA"
$`GO:0051721`$Ontology
[1] "MF"
>
Marc Carlson kirjoitti 2.10.2008 kello 19.59:
> Hi Jukka,
>
> Can you please give us the results of calling sessionInfo()? From
> what
> I can see below it looks like you are using a custom annotation
> package. Is that correct?
>
> Marc
>
>
>
>
> Jukka Hiissa wrote:
>> Dear BioC users,
>>
>> I am having problems with the getOntology-function (annotate-
>> package v.
>> 1.18 ) The command
>>
>> getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" )
>> [1] "GO:0032515" "GO:0032516"
>>
>> returns two GO identifiers, but they are not correct since their
>> ontologies are in fact NA
>>
>> $`GO:0032515`
>> $`GO:0032515`$GOID
>> [1] "GO:0032515"
>> $`GO:0032515`$Evidence
>> [1] "IDA"
>> $`GO:0032515`$Ontology
>> [1] NA
>>
>> $`GO:0032516`
>> $`GO:0032516`$GOID
>> [1] "GO:0032516"
>> $`GO:0032516`$Evidence
>> [1] "IDA"
>> $`GO:0032516`$Ontology
>> [1] NA
>>
>> I looked at the getOntology source code and I think that the
>> problem is
>> that the NAs are removed from the index vector but not from the list
>> containing the GO-elements. The last two lines in the getOntology
>> function are
>>
>> onts = onts[!is.na(onts)]
>> unique(names(inlist[onts %in% which]))
>>
>> where the onts contains the ontology labels, e.g.
>>
>> GO:0000159 GO:0005524 GO:0005625 GO:0008160 GO:0008601 GO:0008601
>> NA "MF" "CC" "MF" "MF" "MF"
>> GO:0016887 GO:0019211 GO:0032515 GO:0032516 GO:0035307 GO:0035308
>> "MF" "MF" NA NA "BP" "BP"
>> GO:0042803 GO:0046982 GO:0051721
>> "MF" "MF" "MF"
>>
>> After the NAs are removed from the onts vector the indexes of the two
>> BP-ontology cases are 8 and 9, but these are not the correct
>> indexes for
>> the inlist list, which still contains the three missing ontology
>> cases.
>>
>> names( inlist )
>> [1] "GO:0000159" "GO:0005524" "GO:0005625" "GO:0008160" "GO:0008601"
>> [6] "GO:0008601" "GO:0016887" "GO:0019211" "GO:0032515" "GO:0032516"
>> [11] "GO:0035307" "GO:0035308" "GO:0042803" "GO:0046982" "GO:0051721
>>
>> Best regards,
>> Jukka Hiissa
>>
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>
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