Usually, Deseq2 analysis gives log2 fold change calculation based on Mean. If I want to get log2 fold change based on the median,What should be the changes I have to make in the code? or what should be the code for that purpose?

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Can you say more about the motivation for using the median? If you care mostly about the ranks, in our lab we have had good results on real and simulated data with SAMseq at gene level analysis and our extension Swish for isoform level analysis.