hi,



> I was expecting that (having no replicates, for several conditions of a
>> single factor/variable) using a dispersion model built from all my samples
>> will increase the number of DE genes found with respect to a single
>> pairwise analysis.
>>
>>
>
>
Adding C and D to the analysis can either decrease or increase the
dispersion estimates for a given gene, for example if the counts for C and
D are close to or far from the counts for A and B.

Mike

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