[BioC] Problems creating topGOdata object!
Valerie Obenchain
vobencha at fhcrc.org
Tue Sep 20 17:22:20 CEST 2011
I should have carried the example a bit further to demonstrate the piece
of code you were trying to run,
geneID2GO<- readMappings(file = system.file("examples/geneid2go.map", package = "topGO"))
GO2geneID<- inverseList(geneID2GO)
geneNames<- names(geneID2GO)
myInterestingGenes<- sample(geneNames, length(geneNames)/10)
geneList<- factor(as.integer(geneNames %in% myInterestingGenes))
names(geneList)<- geneNames
GOdata<- new("topGOdata", ontology = "BP", allGenes = geneList, annot = annFUN.gene2GO,
gene2GO = geneID2GO)
> GOdata
------------------------- topGOdata object -------------------------
Description:
-
Ontology:
- BP
100 available genes (all genes from the array):
- symbol: 068724 119608 049239 067829 106331 ...
- 10 significant genes.
82 feasible genes (genes that can be used in the analysis):
- symbol: 068724 119608 049239 067829 106331 ...
- 9 significant genes.
GO graph (nodes with at least 1 genes):
- a graph with directed edges
- number of nodes = 886
- number of edges = 1671
------------------------- topGOdata object -------------------------
Valerie
On 09/20/2011 08:12 AM, Valerie Obenchain wrote:
> Hi Gabriel,
>
> The first step would be up update your version of R and BioC packages.
> The current version is R-2.13 and a new release will be coming out in
> late October.
>
> I do not get any warnings/errors in the vignette example with R-2.13,
>
> library(topGO)
> library(ALL)
> data(ALL)
> data(geneList)
> affyLib <- paste(annotation(ALL), "db", sep = ".")
> library(package = affyLib, character.only = TRUE)
>
> sampleGOdata <- new("topGOdata",
> description = "Simple session", ontology = "BP",
> allGenes = geneList, geneSel = topDiffGenes,
> nodeSize = 10,
> annot = annFUN.db, affyLib = affyLib)
>
> > sampleGOdata
>
> ------------------------- topGOdata object -------------------------
>
> Description:
> - Simple session
>
> Ontology:
> - BP
>
> 323 available genes (all genes from the array):
> - symbol: 1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at ...
> - score : 1 1 0.62238 0.541224 1 ...
> - 50 significant genes.
>
> 315 feasible genes (genes that can be used in the analysis):
> - symbol: 1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at ...
> - score : 1 1 0.62238 0.541224 1 ...
> - 50 significant genes.
>
> GO graph (nodes with at least 10 genes):
> - a graph with directed edges
> - number of nodes = 713
> - number of edges = 1424
>
> ------------------------- topGOdata object -------------------------
>
>
> > sessionInfo()
> R version 2.13.0 Patched (2011-04-14 r55448)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hgu95av2.db_2.5.0 org.Hs.eg.db_2.5.0 ALL_1.4.7
> [4] topGO_2.4.0 SparseM_0.89 GO.db_2.5.0
> [7] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.0
> [10] Biobase_2.12.0 graph_1.30.0
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.0 lattice_0.19-23 tools_2.13.0
>
>
> Valerie
>
>
> On 09/20/2011 05:59 AM, gabriel teku wrote:
>> Hi List,
>> I have been trying to create a topGOdata object as follows:
>>
>> *GOdata<- new("topGOdata", ontology = "BP", allGenes = geneList, annot
>> =annFUN.gene2GO, gene2GO = gene2GO)*
>>
>> where, geneList and gene2GO are as described in the topGO docs.
>>
>> However, I keep getting the following error:
>>
>> Building most specific GOs .....
>> Error in annotationFun(ontology, .Object at allGenes, ...) :
>> argument "gene2GO" is missing, with no default
>>
>>
>> I would appreciate any quick help on this issue.
>>
>> Below is my sessionInfo:
>>
>>> sessionInfo()
>> R version 2.12.1 (2010-12-16)
>> Platform: i386-redhat-linux-gnu (32-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] topGO_2.2.0 SparseM_0.89 GO.db_2.4.5
>> [4] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.12.0
>> [7] Biobase_2.10.0 graph_1.28.0 biomaRt_2.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.12.1 lattice_0.19-13 RCurl_1.5-0 tools_2.12.1
>> [5] XML_3.2-0
>>
>>
>>
>>
>> Contact me: [image: Google Talk] gabbyteku [image: Skype] gabbyboy30
>> [image:
>> MSN] gabbyteks at hotmail.com [image: Y! messenger] gabbyteku
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