Greetings,

I'm getting the following error when calling glmQLFTest()

> qlf <- glmQLFTest(fit,contrast=cont.matrix)
Error in data.frame(logFC = logFC, logCPM = glmfit$AveLogCPM, LR = LR,  :
  'row.names' should specify one of the variables

> traceback()
4: stop("'row.names' should specify one of the variables")
3: data.frame(logFC = logFC, logCPM = glmfit$AveLogCPM, LR = LR, 
       PValue = LRT.pvalue, row.names = rn)
2: glmLRT(pois.fit, coef = coef, contrast = contrast)
1: glmQLFTest(fit, contrast = cont.matrix)

I think the error is due to the call to  .isBelowPoissonBound() only returning a single row for my data set.   My guess is that the problem is that in glmLRT() the call

logFC <- drop((glmfit$coefficients %*% contrast)/log(2))

will produce a vector rather than a matrix, which eventually results in the error from data.frame().

I have an example data set & code at this gist https://gist.github.com/drpowell/ac473045cfea8b489d49e645d3239a53#file-dge-r

Thanks,

-- David

A simpler reproducible example is this:

library(edgeR)
example(glmFit)
glmLRT(fit[1,], contrast=diag(2))

... and yes, it is caused by drop when computing logFC. The simplest solution would be to just get rid of drop; if we want a vector (e.g., when there is only one coefficient to test), we can just coerce it directly.

Thanks David. I have committed a fix to edgeR 3.20.1 for Bioconductor 3.6.