TopGo, factor of 1 means

[tinguzman]

Hi,

I'm trying to do GO enrichment analysis using topgo, but i've encountered a problem, read below. what does factor w/ level 1 mean? it says that i should have 2 level factors. how can I fix this?


> myInterestingGenes <- as.vector(AvsB$genes)
> geneList <- factor(as.integer(geneNames %in% myInterestingGenes))
> names(geneList) <- geneNames
> names
function (x) .Primitive("names")
> str(geneList)
Factor w/ 1 level "0": 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "names")= chr [1:18756] "Genes" "c10020_g1" "c10035_g1" "c10052_g1" ...


Error in .local(.Object, ...) : allGenes must be a factor with 2 levels

[Jeremy]

Your problem is probably from this line

geneList <- factor(as.integer(geneNames %in% myInterestingGenes))

geneNames %in% myInterestingGenes will return a vector of TRUE / FALSE of length length(geneNames)
converting that to an interger will make it 1's and 0's. In this case it seems that every element of geneNames overlaps with an element in myInterestingGenes resulting a vector of 1's which you then change to a factor. If you are supposed to have a vector of only 1's then you can set the levels in the factor call to make sure that the factor has 2 levels, but then you still only one type which is probably not what you intend.