Dear Bioconductor list,

I have a list of genes from a mouse array (custom design) for which I want
to perform an analysis with topGO. The package example is running fine and
I have read the vignettes (though I've probably missed something) but when
running my own data an error is generated that seems to be related to my
custom Gene-to-GO map.

The results are a table with several annotations and custom measure of
significance. I've created a named vector (list) containing all the genes
present in the array (ensembl IDs) with the corresponding measure of
significance - geneList.

geneList <- abs(data[ ,2])
names(geneList) <- data[ ,1]
geneList[1:5]
ENSMUSG00000025903 ENSMUSG00000025903 ENSMUSG00000025903 ENSMUSG00000025903
ENSMUSG00000033813
0.11               0.36               0.32               0.07
0.08

is(geneList)
[1] "numeric"          "vector"           "atomic"
"EnumerationValue" "numeric or NULL"  "vectorORfactor"

summary(geneList)
Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
0.0100  0.0600  0.2000  0.4568  0.5600 18.1600

# a function was then defined to select the significant genes - as in the
vignette

topDiffGenes <- function(allScore) {
  return(allScore > 1)
  }


x <- topDiffGenes(geneList)
sum(x)

# so far so good
# because this is a custom array the GO annotation was extracted from
ensemble using BiomaRt.
# ensembl61 was used because of the gene format in my results

ensembl61=useMart('ENSEMBL_MART_ENSEMBL',dataset='mmusculus_gene_ensembl',
                  host='feb2011.archive.ensembl.org')

test.GO.BP <- getBM(attributes = c("ensembl_gene_id",
"go_biological_process_id"), filters = "ensembl_gene_id", values =
All.genes.Ens,
                 mart = ensembl61)
head(test.GO.BP)

ensembl_gene_id go_biological_process_id
1 ENSMUSG00000054310               GO:0006355
2 ENSMUSG00000054728
3 ENSMUSG00000021368               GO:0032313
4 ENSMUSG00000021368               GO:0031398
5 ENSMUSG00000051335               GO:0055114
6 ENSMUSG00000051335               GO:0008152

# but when creating the topGO object a problem appears:

GOdata <- new("topGOdata",
              description = "GO analysis Test",
              ontology = "BP",
              allGenes = geneList,
              geneSel = topDiffGenes,
              annot = annFUN.gene2GO,
              nodeSize = 5,
              gene2GO = test.GO.BP)

Building most specific GOs ..... ( 0 GO terms found. )

Build GO DAG topology .......... ( 0 GO terms and 0 relations. )
Error in if (is.na(index) || index < 0 || index > length(nd))
stop(paste("selected vertex",  :
  missing value where TRUE/FALSE needed

>From reading the vignette I think that the object test.GO.BP, a data.frame,
needs to be convert to a list in which each gene corresponds  to several GO
terms:

List of 6
$ 068724: chr [1:5] "GO:0005488" "GO:0003774" "GO:0001539" "GO:0006935" ...
$ 119608: chr [1:6] "GO:0005634" "GO:0030528" "GO:0006355" "GO:0045449" ...
$ 049239: chr [1:13] "GO:0016787" "GO:0017057" "GO:0005975" "GO:0005783" ...
$ 067829: chr [1:16] "GO:0045926" "GO:0016616" "GO:0000287" "GO:0030145" ...
$ 106331: chr [1:10] "GO:0043565" "GO:0000122" "GO:0003700" "GO:0005634" ...
$ 214717: chr [1:7] "GO:0004803" "GO:0005634" "GO:0008270" "GO:0003677" ...

Is this what I need to do next? If how to do it? Or is it something else?

Any help will be appreciated.

Session info:
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] plyr_1.7.1                           genefilter_1.36.0
   hgu95av2_2.2.0                       hgu95av2.db_2.6.3
 [5] org.Hs.eg.db_2.6.4                   affyio_1.22.0
   affydata_1.11.15                     affy_1.32.1
 [9] multtest_2.10.0                      ALL_1.4.11
    topGO_2.6.0                          SparseM_0.91

[13] GO.db_2.6.1                          graph_1.32.0
    mogene10sttranscriptcluster.db_8.0.1 org.Mm.eg.db_2.6.4

[17] RSQLite_0.11.1                       DBI_0.2-5
   AnnotationDbi_1.16.19                Biobase_2.14.0
[21] BiocInstaller_1.2.1                  biomaRt_2.10.0
    Biostrings_2.22.0                    GenomicRanges_1.6.7

[25] IRanges_1.12.6

loaded via a namespace (and not attached):
 [1] MASS_7.3-17           RColorBrewer_1.0-5    RCurl_1.91-1
 XML_3.9-4             annotate_1.32.3       colorspace_1.1-1
 dichromat_1.2-4
 [8] digest_0.5.2          ggplot2_0.9.0         grid_2.14.2
lattice_0.20-6        memoise_0.1           munsell_0.3
preprocessCore_1.16.0
[15] proto_0.3-9.2         reshape2_1.2.1        scales_0.2.0
 splines_2.14.2        stringr_0.6           survival_2.36-12
 tools_2.14.2
[22] xtable_1.7-0          zlibbioc_1.0.1

-- 
-- 
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domingue@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

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