topgo rnaseq error

Question

[tarek.mohamed]

Hi,

I am trying to use topgo to do GO analysis for a RNA-seq data I have analyzed using DESeq2.

I got this error

Error in if is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ", : missing value where TRUE/FALSE needed

Here is my script

>biocLite("topGO")
>library(topGO)

>library(org.Hs.eg.db)

>all <- res$padj

>names(all) <- rownames(res)
>all <- na.omit(all)
>head(all)
>names(all)
>str(res$padj)
>head(res)
>GOdata <- new("topGOdata",ontology = "CC", allGenes = all, geneSel=function(p) p < 0.01, description ="CardiomyocytesGenes", annot=annFUN.org, mapping="org.Hs.eg.db", ID="Ensembl") 

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("vertex is not in graph: ",  : 
  missing value where TRUE/FALSE needed

[tarek.mohamed]

Hi ,

I knew what was the mistake.

I have added gene names instead of ensembl gene id to my results, that is why the mapping did not work.

Thanks

Tarek

Answer 1

[tarek.mohamed]

Hi ,

I knew what was the mistake.

I have added gene names instead of ensembl gene id to my results, that is why the mapping did not work.

Thanks

Tarek