Hi all,

I have a quite novice question:

I am aware that ENSEMBL has recently release a new version (ENSEMBL 91). Since then I have been having trouble reproducing my results from the GO analysis (using topGO package). Potentially, this could be due to me upgrading Bioconductor as well (but I think it is less likely).

I am attaching here the 2 sets of results (original and new). For the new results, I even try to use the archived version of ENSEMBL. However, somehow the results are still not the same.

For example, for the annotated column, the term "mRNA catabolic process" has 218 terms in the original but it has 313 terms in the new result ??? This must be due to ENSEMBL database because they both have the same input data files.

Anyone has any advice/suggestion?

    bm <- useMart("ensembl", host = "http://aug2017.archive.ensembl.org", 
    dataset = "hsapiens_gene_ensembl")
    EG2GO <- getBM(mart=bm, 
    attributes=c('ensembl_gene_id','external_gene_name','go_id'))
    EG2GO <- EG2GO[EG2GO$go_id != '',]
    name2GO <- by(EG2GO$go_id,EG2GO$external_gene_name,function(x) 
    as.character(x))
    
    geneuniverse<-as.character(rownames(LN_cells_no_zero))
    geneofinterest<-as.character(ductruong_l0_norm$Significant_Genes)
    genelist<-factor(as.integer(geneuniverse %in% geneofinterest))
    names(genelist)<-geneuniverse
    godata<-new("topGOdata", description = "Significant_Genes_L0norm", 
    allGenes = genelist, ontology="BP", nodeSize = 10, annot = 
    annFUN.gene2GO, gene2GO = name2GO)

See A: biomaRt is not working

Hi all,

Thank you for your answer.

I have upgraded my biomaRt to the newest version. It seems like somehow the GO annotation is different that affects my results. Does ENSEMBL modify their archive servers as well?