[BioC] DEXSeq design formula

[Simone]

Hello!

Just a quick question regarding DEXSeq:

I have more variables in my experiment (9 samples), i.e. 3 different
celltypes (variable of interest) taken from 4 different patients. To
take into account when samples come from the same patient I included
an additional factor to the sampleData table.

I understand that I have to use the following formulae when it comes
to testing for differential exon usage:

formulaFullModel = ~ sample + exon + patient:exon + celltype:exon
formulaReducedModel = ~ sample + exon + patient:exon

And I assume (but  it's not quite clear to me from reading the
vignette) that I also have to add the additional patient variable to
the design already when creating the DEXSeqDataSetFromHTSeq:

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

Is this correct?

Best,
Simone