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Heike Pospisil
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310
@heike-pospisil-1097
Last seen 10.2 years ago
Hello list,
I am trying to use topGO for GO enrichment analysis. I have data from
an
array which is still not supported by BioC (maize array).
I have a mapping of genes to GO terms named go_list:
$TM00000001
[1] "GO:0009058" "GO:0016757"
$TM00000002
[1] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" "GO:0016563"
[6] "GO:0009737" "GO:0045449" "GO:0010072" "GO:0046982" "GO:0009651"
[11] "GO:0009733" "GO:0009723" "GO:0009734" "GO:0048527" "GO:0042803"
[16] "GO:0009867" "GO:0010150" "GO:0009825" "GO:0009908" "GO:0003713"
[21] "GO:0051607" "GO:0009790" "GO:0010014" "GO:0048467" "GO:0030528"
[26] "GO:0009741" "GO:0009735" "GO:0010089" "GO:0009834" "GO:0009901"
[31] "GO:0009611" "GO:0008361" "GO:0009416" "GO:0009620" "GO:0009744"
[36] "GO:0009753" "GO:0009751" "GO:0010199"
Moreover, the geneList is the named factor that indicates which genes
are interested:
> str(geneList)
Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "names")= chr [1:56321] "MZ00000001" "MZ00000002"
"MZ00000003" "MZ00000004" ...
I have used annFUN.gene2GO as an annotation function:
GOdata<-new("topGOdata",ontology="MF",allGenes=geneList,annot=annFUN.g
ene2GO,gene2GO=go_list)
Unfortunately, I got the following error message:
Building most specific GOs .....Error in order(allGO) : argument 1 is
not a vector
Does anybody have an idea what is wrong in my code?
Thanks and best,
Heike