[BioC] topGO and GOstats conflict
Dick Beyer
dbeyer at u.washington.edu
Mon Mar 31 17:33:04 CEST 2008
Hi Robert,
Here is a traceback of the error I found.
library(topGO)
library(GOstats)
BP.GOdataEG <- list(new("topGOdata", ontology = "BP", allGenes =
geneListEG[[1]],
+ description = paste("GO BP analysis of 08.3.29 MCAT proteins",labs[1]),
+ annot = annFUN.gene2GO, gene2GO = gene2GO))
Building most specific GOs ..... ( 3337 GO terms found. )
Build GO DAG topology ..........Error in as.vector(x, "list") : cannot coerce
to vector
> traceback()
8: as.list.default(GOParents)
7: as.list(GOParents)
6: GO.getRoot(GOParents)
5: buildGOgraph.topology(mostSpecificGOs, ontology)
4: .local(.Object, ...)
3: initialize(value, ...)
2: initialize(value, ...)
1: new("topGOdata", ontology = "BP", allGenes = geneListEG[[1]],
description = paste("GO BP analysis of 08.3.29 MCAT proteins",
labs[1]), annot = annFUN.gene2GO, gene2GO = gene2GO)
sessionInfo()
R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] splines tools stats graphics grDevices utils datasets
methods base other attached packages:
[1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 survival_2.34
RBGL_1.14.0 [6] annotate_1.16.0 xtable_1.5-1 GO.db_2.0.0
topGO_1.4.0 SparseM_0.73 [11] AnnotationDbi_1.0.6 RSQLite_0.6-3
DBI_0.2-3 GO_2.0.0 Biobase_1.16.0 [16] graph_1.16.1
loaded via a namespace (and not attached):
[1] cluster_1.11.9
Cheers,
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 Mon, 31 Mar 2008, Robert Gentleman wrote:
> if you were to run traceback() right after the error, that would help us pin
> point the actual code that was being evaluated...
>
> Dick Beyer wrote:
>> Hi Robert,
>>
>> I re-ran my code to see the error message when I load GOstats after topGO.
>>
>>> BP.GOdataEG <- list() for(i in 1:5){
>> + BP.GOdataEG[i] <- list(new("topGOdata", ontology = "BP", allGenes =
>> geneListEG[[i]],
>> + description = paste("GO BP analysis of 08.3.29 MCAT
>> proteins",labs[i]),
>> + annot = annFUN.gene2GO, gene2GO = gene2GO))
>> + }
>>
>> Building most specific GOs ..... ( 3337 GO terms found. )
>>
>> Build GO DAG topology ..........Error in as.vector(x, "list") : cannot
>> coerce to vector
>>
>> sessionInfo()
>> R version 2.6.1 (2007-11-26) i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] splines tools stats graphics grDevices utils datasets
>> methods base
>>
>> other attached packages:
>> [1] GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0
>> survival_2.34
>> [5] RBGL_1.14.0 annotate_1.16.0 xtable_1.5-1
>> GO.db_2.0.0
>> [9] topGO_1.4.0 SparseM_0.73 AnnotationDbi_1.0.6
>> RSQLite_0.6-3 [13] DBI_0.2-3 GO_2.0.0 Biobase_1.16.0
>> graph_1.16.1
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.9
>>
>>
>> If I restart my R session and load GOstats then topGO, the above code
>> works fine. So you were right about this being a possible NAMESPACE
>> issue.
>>
>> Cheers,
>> 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 Sun, 30 Mar 2008, Robert Gentleman wrote:
>>
>>> Thanks for the note Dick
>>>
>>> Dick Beyer wrote:
>>>> Just a note for people to find when they search the mail about a
>>>> conflict between topGO and GOstats.
>>>>
>>>> I was running topGO successfully, then I loaded GOstats so I could
>>>> plot some DAGs via GOGraph. That worked just fine. I then tried to
>>>> rerun some topGO code and was unable to execute soemthing like this:
>>>>
>>>>
>>>> BP.GOdataEG <- list() for(i in 1:5){
>>>> BP.GOdataEG[i] <- list(new("topGOdata", ontology = "BP", allGenes =
>>>> geneListEG[[i]],
>>>> description = paste("GO BP analysis of 08.3.29 MCAT
>>>> proteins",labs[i]),
>>>> annot = annFUN.gene2GO, gene2GO = gene2GO))
>>>> }
>>>>
>>>> I would get the message of "Building most specific GOs, but then I'd
>>>> get an error on the "Build GO DAG topology" step saying something like
>>>> couldn't make a vector from a list. A bit obscure to me. I haven't
>>>> read the fine print on topGO or GOstats, so maybe having both packages
>>>> loaded at the same time is forbidden. Anyway, the fix is easy, just
>>>> run one or the other.
>>>>
>>>
>>> that suggests that topGO is not using a NAMESPACE (Adrian, your package
>>> would likely benefit from having one, so that you have better control
>>> over which functions are getting picked up). The purpose of NAMESPACEs
>>> is to ensure that this does not happen. I suspect, but am not sure that
>>> if you load GOstats first, then topGO that you would not have trouble.
>>> If you have the energy to try that and report back (but with the error,
>>> if there is one, not a summary) that could help.
>>>
>>> thanks
>>> Robert
>>>
>>>
>>>> sessionInfo()
>>>> R version 2.6.1 (2007-11-26) i386-pc-mingw32
>>>>
>>>> locale:
>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>>> States.1252;LC_MONETARY=English_United
>>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>>
>>>> attached base packages:
>>>> [1] tools stats graphics grDevices utils datasets
>>>> methods base
>>>>
>>>> other attached packages:
>>>> [1] topGO_1.4.0 SparseM_0.73 AnnotationDbi_1.0.6
>>>> RSQLite_0.6-3 DBI_0.2-3 [6] GO_2.0.0 Biobase_1.16.0
>>>> graph_1.16.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] cluster_1.11.9
>>>>
>>>> Cheers,
>>>> 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
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>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>
>>>
>>> --
>>> Robert Gentleman, PhD
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M2-B876
>>> PO Box 19024
>>> Seattle, Washington 98109-1024
>>> 206-667-7700
>>> rgentlem at fhcrc.org
>>>
>>
>>
>>
>
> -- Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
>
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