I have a clarification question on how the average expression versus dispersion curve is generated. From the paper, it says that Deseq2 uses 'all samples' in making the plot, but is that all samples for a given sample type (genotype) or is it all samples regardless of genotype?
I am worried that gene dispersion information is being shared between genotypes, and I am wondering if this is valid. I understand that DESeq2 uses the correlation between average gene expression and dispersion for dispersion shrinkage, but does this assumption hold true between genotypes?
Quote from DESeq2 paper:
"Our DESeq method  detects and corrects dispersion estimates that are too low through modeling of the dependence of the dispersion on the average expression strength over all samples." Deseq2 Paper