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  • DESeq estimation of dispertion pooled CR

    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.

    Code:
    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 !!

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