Hi,

I have a table of results from DEXSeq, but don't have the row data. I would like to plot some genes, using your plotDEXSeq function, but if I simply enter the dataframe I have, it returns an error

plotDEXSeq(DF, "Jak2", displayTranscripts=TRUE, legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 )

Error in plotDEXSeq(as.matrix(DF), "Jak2", displayTranscripts = TRUE, : is(object, "DEXSeqResults") | is(object, "DEXSeqDataSet") is not TRUE

I'd be happy to run DEXSeq from the information I have in the table.

dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile )

I imagine there is a way as I have the counts. Something equivalent to DESeqDataSetFromMatrix. But I can't make it work. Here are the column contained in the table:

• groupID featureID
  exonBaseMean
  dispersion
  stat
  pvalue
  padj
  genotype1
  genotype2
  log2foldgenotype2genotype1
  genomicData.seqnames
  genomicData.start
  genomicData.end genomicData.width
  genomicData.strand
  countData.Sample1genotype1
  countData.Sample3genotype1
  countData.Sample4genotype1
  countData.Sample7genotype1
  countData.Sample1genotype2
  countData.Sample3genotype2
  countData.Sample4genotype2
  countData.Sample7genotype2
  transcripts

row names are groupID:featureID

Is there a way to exploit this? Thank you for your help

The first argument in your call to "plotDEXSeq" should not be a data frame, but the DEXSeqDataSet object, i.e., "dxd". Try replacing "DF" with "dxd" in the call.