**0**wrote:

Hi,

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 `DEXseq`

and `StageR`

?

Thank You

**22k**• written 5 months ago by rbenel •

**0**