Error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values

[mdozmorov]

I'm using DEXSeq results generated by the rnasplice Nextflow pipeline. The pipeline generates .RDS objects, with DEXSeqDataSet and DEXSeqResults. I tried plotting some genes of interest but getting:

Error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : 
  need finite 'ylim' values
In addition: Warning messages:
1: In max(coeff, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In vst(coeff, object) :
  Dispersion function not parametric, applying log2(x+ 1) instead of vst...
3: In max(matr) : no non-missing arguments to max; returning -Inf

This error occurs if using the DEXSeqResults object and after processing the DEXSeqDataSet object. I tried debugging the plotDEXSeq function, but it gets too complex. Here's a reproducible example using demo.rds

library(DEXSeq)
res <- readRDS("demo.rds")
plotDEXSeq(res, "ENSG00000291317")

This happens with other genes I tried. Please, help.

[Fabriesh]

I ran into the same problem when working with a manually constructed DEXSeqDataSet. It seems that the rowRanges object within the DEXSeqDataSet and within the resulting DEXSeqResults is essential for the plotDEXseq() and DEXSeqHTML() functions. I had to add the rowRanges manually using the featureRanges accessor in the DEXSeqDataSet() constructor function, using the corresponding values for seqnames=, ranges= and strand= that I got from my original FeatureCounts output.

[piplus2]

That occurs in DTU where as correctly pointed by @Fabriesh the ranges are missing. Usually, we don't want that plot for transcripts because it's designed to display the exon usage.