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topGO error : could not find function "annotationFun"
... Hi, >Where am I going wrong?! I am trying to create topGO object by custom annotations, But am facing difficulty again and again.  > GOdata <- new("topGOdata", ontology = "BP", allGenes = P_values, geneSelectionFun = topDiffGenes, description = "Simple session", annot = annFUN.gene2GO(wh ...
topgo R written 3 months ago by User0
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Comment: C: AffyLib query in topGO
... 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, ... ...
written 3 months ago by User0
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Comment: C: AffyLib query in topGO
... 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 LO ...
written 3 months ago by User0
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AffyLib query in topGO
... 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 ...
affy topgo written 4 months ago by User0 • updated 4 months ago by James W. MacDonald46k

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