Greetings,
I have a sample with four different conditions:

1uE, 10 uE, 100uE, 500uE

The conditions are analyzed as pairs:
1uE vs10 uE
1uE vs 100 uE
1uE vs 500uE

Using the examples in the DESeq tutorial it appears that I would have to
analyze these pairs as having no replicates but I'm thinking I really have
four replicates. Is there a way to calculate the dispersion using all of
the data and then extract the pairs for DE analysis?

Thanks,
Bill

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