Goseq - Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed

Question

[ryme]

Hello guys!

I am having some troubles running GO analysis using goseq package in r. I am using goseq to analyze my human RNAseq data. I have used the DESEQ package to perform the differential expression analysis. I am trying to use the Fitting the Probability Weighting Function (PWF) :

pwf=nullp(genes,"hg19","ensGene")

But an error occurred as following:

Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed

I checked my data, there are no NA characters in them.

Could anyone help me, please!

I am new to r and I have never done this type of analysis before, that's why I am struggling a bit.

Preparing the data:

rowsum.threshold <- 1 
fdr.threshold <- 0.1 
rs <- rowSums(counts(dds))
dds <- dds[ rs > rowsum.threshold ,]
dds <- DESeq(dds)
res <- results(dds, independentFiltering=FALSE) 
assayed.genes <- rownames(res)
de.genes <- rownames(res)[ which(res$padj < fdr.threshold) ]

Running goseq:

Fitting the Probability Weighting Function (PWF):

pwf=nullp(de.genes,"hg19","ensGene")

Error:

Error in if (matched_frac == 0) { : missing value where TRUE/FALSE needed