Question

topGO error: allGenes should be a factor or a numeric vector

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ccha ▴ 10

@ccha-23888

Last seen 3.6 years ago

Hello, I'm trying to perform GO-term analysis with some differentially expressed genes using the topGO package and following the steps in the booklet. Currently I am having trouble trying to prepare the input data.

This is my code taken from the booklet, but with my particular set of genes:

sampleGOdata <- new("topGOdata", ontology = "BP", allGenes = cluster2TOPgo_GeneList, geneSel = topDiffGenes, nodeSize = 10, annot = org.Mm.eg.db)

However when I run this, it comes up with "Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector"

This is what my gene list looks like (entrez ID as row names and adjusted p values down the column versus their example gene list.

Can someone explain to me what I've done wrong and how I can fix this issue?

topGO topgo GO term analysis • 5.8k views

ADD COMMENT • link updated 3.8 years ago by Kevin Blighe ★ 3.9k • written 3.8 years ago by ccha ▴ 10

score 1 · Answer 1 · 2020-07-19

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Kevin Blighe ★ 3.9k

@kevin

Last seen 9 days ago

Republic of Ireland

The allGenes parameter should specify a named vector, with the values of this vector being [typically] p-values, and the names being gene names. It should look like this:

library(topGO)
library(ALL)
data(geneList)
head(geneList)
1095_s_at   1130_at   1196_at 1329_s_at 1340_s_at 1342_g_at 
1.0000000 1.0000000 0.6223795 0.5412240 1.0000000 1.0000000

So, please verify the content of your cluster2TOPgo_GeneList variable.

Kevin

ADD COMMENT • link 3.8 years ago Kevin Blighe ★ 3.9k

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Hi Kevin, Thanks for your reply. When I run (headGeneList), it comes up with the exact same output as your code. However, when I run the head of my genelist, it comes up with this. Does this mean I have to transpose my dataframe so that the genes are columns and the pvalues are the first row?

ADD REPLY • link 3.8 years ago ccha ▴ 10

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It looks like it is in the incorrect format, yes. A named vector is created like this:

x <- c(1,2,3,4)
names(x) <- c('A','B','C','D')

ADD REPLY • link 3.8 years ago Kevin Blighe ★ 3.9k

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I've turned my dataframe into a named vector, but still seem to get the same error. Here's the head of my vector (cluster2genelistv) and what it looks like when I view it.

enter image description here

ADD REPLY • link 3.8 years ago ccha ▴ 10

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Thanks. Looks like the values in cluster2genelistv should be numeric. Currently, they are encoded as characters.

ADD REPLY • link 3.8 years ago Kevin Blighe ★ 3.9k

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Yep, that seemed to have worked by changing it to as. numeric instead of as.character: cluster2genelistv <- setNames(as.numeric(cluster2TOPgoGeneList$padj), rownames(cluster2TOPgoGeneList))

I think the input for allGenes is all good now (as indicated by the green bar when I run the code) but unfortunately it comes up with another error.

sampleGOdata <- new("topGOdata", ontology = "BP", allGenes = cluster2genelistv, geneSel = topDiffGenes, nodeSize = 10,  annot = annFUN.org, mapping="org.Mm.eg.db", ID = "SYMBOL")

Building most specific GOs ..... ( 0 GO terms found. )

Build GO DAG topology .......... ( 0 GO terms and 0 relations. ) Nothing to do: Error in split.default(names(sort(nl)), f.index) : first argument must be a vector

ADD REPLY • link 3.8 years ago ccha ▴ 10

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The next problem is that you have specified ID = "SYMBOL", but you are using [I assume] Entrez IDs in your input named vector, cluster2genelistv. So, you could try ID = "ENTREZ"

Actually, I usually run topGo in a different way - see here on Biostars: https://www.biostars.org/p/350710/#350712

ADD REPLY • link 3.8 years ago Kevin Blighe ★ 3.9k

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Thank you kindly - changing ID to ENTREZ seemed to do the trick! The code from the Biostars post worked like a charm too, and was even able to get the graph.

ADD REPLY • link 3.8 years ago ccha ▴ 10