DESeq estimation of dispertion pooled CR

[raphael123]

Hi, everyone, sorry if it s a stupid question.
My dataset is miRNA's, we are using DESeq to check a case versus control in two different condition.
Since my samples are all paired between conditions I want to estimate dispertion using the fact that I have two sample per subjects.

cds=estimateDispersions(
                 cds,
                 method='pooled-CR',
                 sharingMode="maximum",
                 fitType="local",
                 modelFormula = count ~ miRNAdesign$subject
)
cds2=cds[,is_condition1]

exact test and blablabla ...

I am not sure if what I am doing is good, could you make me understand my own command ?

Thank you !!