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@user-15063
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Hi,
While creating an object for topGO as :
sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP", allGenes = P_values, geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.db, affyLib = affyLib)
what if there is no annotation database available for that particular organism in bioconductor?
Can someone tell me if there is any alternative available to use instead of the annotation databases of affylib(affyLib = affyLib).
Any guidance will be appreciated.
Thank you!
I have followed the steps mentioned in the documents (both 2016 and 2017) provided in the vignette for enrichment analysis by topGO.
> library(topGO) > geneList <- read.xlsx("genelist.xlsx", 1) > head(geneList) Gene_ID P_value 1 LOC_Os01g01120.1 0.0023 2 LOC_Os01g01120.1 0.0034 3 LOC_Os01g01120.1 0.0071 4 LOC_Os01g01120.1 0.0210 5 LOC_Os01g13120.1 0.0163 6 LOC_Os01g18210.1 0.0042 > rn <- paste(geneList[,1], sep="") > P_values=geneList[,-1] > names(P_values)<-rn > head(P_values) LOC_Os01g01120.1 LOC_Os01g01120.1 LOC_Os01g01120.1 LOC_Os01g01120.1 LOC_Os01g13120.1 LOC_Os01g18210.1 0.0023 0.0034 0.0071 0.0210 0.0163 0.0042 > sum(topDiffGenes(P_values)) [1] 167 > geneid2GO <- read.xlsx("genetoGO.xlsx", 1) > head(geneid2GO) Gene_ID GO_ID 1 LOC_Os01g01120.1 GO:0008152 2 LOC_Os01g01120.1 GO:0008152 3 LOC_Os01g01120.1 GO:0008152 4 LOC_Os01g01120.1 GO:0008152 5 LOC_Os01g13120.1 GO:0005773 6 LOC_Os01g18210.1 GO:0005576 > rn1 <- paste(geneid2GO[,1], sep="") > gene2GO = geneid2GO[,-1] > names(gene2GO)<-rn > head(gene2GO) LOC_Os01g01120.1 LOC_Os01g01120.1 LOC_Os01g01120.1 LOC_Os01g01120.1 LOC_Os01g13120.1 LOC_Os01g18210.1 GO:0008152 GO:0008152 GO:0008152 GO:0008152 GO:0005773 GO:0005576 41 Levels: GO:0000003 GO:0000166 GO:0003674 GO:0003677 GO:0003723 GO:0003824 GO:0005488 GO:0005575 ... GO:0030246 > GOdata <- new("topGOdata", ontology = "MF", allGenes = P_values, geneSel = topDiffGenes, annot = annFUN.gene2GO, gene2GO = gene2GO) Building most specific GOs ..... ( 41 GO terms found. ) Build GO DAG topology .......... There are no adj nodes for node: GO:0000003 Error in switch(type, isa = 0, partof = 1, -1) : EXPR must be a length 1 vector_______________________________________________
I am getting this kind of error.
I also tried using:
> GOdata <- new("topGOdata", ontology = "MF", allGenes = P_values, geneSel = topDiffGenes, annot = annFUN.file(file = "GO_genelist_alldata.txt", whichOnto = "MF"), gene2GO = gene2GO) Building most specific GOs ..... Error in annotationFun(ontology, .Object@allGenes, ...) : could not find function "annotationFun"