topgo for 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 getClass(Class, where = topenv(parent.frame())) : 
  “topGOdata” is not a defined class

Here is my script

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

Error in getClass(Class, where = topenv(parent.frame())) : 
  “topGOdata” is not a defined class

Thanks,

Tarek

[Devon Ryan]

You probably want to post this on the bioconductor site instead.

[tarek.mohamed]

Hi,

I have installed the most recent versions for R and Bioconductor and the issue was solved.

thanks

Tarek