[BioC] Problems creating topGOdata object!

[Valerie Obenchain]

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:
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