I was wondering which counts are appropriate to use for plotting the expression of the differential transcripts?
plotDEXSeq is giving me this error, even when using the pre-constructed matrix of counts from the workflow "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification":
plotDEXSeq( dxr2, "ENSG00000000457.13", legend=FALSE, cex.axis=1.2, cex=1.3, lwd=2 ) #legend is false because we have not imported everything from the txdf.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 max(matr) : no non-missing arguments to max; returning -Inf
I am interested in outputting all normalized transcripts that I found to be to differentially expressed.
Further, I have looked at the function
plotDEXseq and it uses
featureCounts, which is just like requesting in Deseq2,
counts(object, normalized = TRUE) of the specific groupID. I can't help but wondering if these counts are OK to graphically represent a *transcript* that was found to be differential expressed following