DEXSeq design formula & estimating dispersion

Question

[hofman.bartlomiej]

Hello everyone,

help me understand the design formula in DEXSeq workflow, in the vignette and manual for creating DEXSeqDataSet object:

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

In my design table I have two columns: sample (individuals) and condition (healthy vs tumor). I want to perform differential exon usage analysis between healthy & tumor conditions. I tried to perform such analysis with design:

~condition+exon+condition:exon

Then i calculated size factors and dispersions in a couple of minutes. When I include the sample in the design calculating dispersions takes forever. My question is what is the purpose of including sample variable into the design formula? Is it necessary for the downstream workflow or can I just leave it my first idea of not including sample in the design.

Thank you very much in advance!