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56 minutes ago by
tarek.mohamed • 0
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
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