TopGo, factor of 1 means

tinguzman · 09-10-2014, 09:10 PM

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 · 09-15-2014, 02:54 AM

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.

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09-10-2014, 09:10 PM	#1
tinguzman Member Location: Philippines Join Date: Aug 2014 Posts: 13	TopGo, factor of 1 means 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

09-15-2014, 02:54 AM	#2
Jeremy Senior Member Location: Pathum Thani, Thailand Join Date: Nov 2009 Posts: 190	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.