[BioC] How many biological replicates might suffice with Cox-Reid estimation in DESeq2 (or edgeR)?

[Michael Muratet]

Greetings

I am working on analyzing the data from an experiment with multiple technical replicates but no biological replicates. FWIW, it's the same data set I have posted about in recent weeks. I think the experiment would benefit greatly from some biological replicates. The question I have is this: given that the dispersion estimator algorithm is able to 'share' data among samples, does anyone know of any experiments or simulations to establish guidelines for a minimum or recommended number of biological replicates smaller than all N samples? The DESeq2 manual says that it employs Cox-Reid for estimating dispersions, is it same implementation as described in McCarthy et al., 2012, or are there some new twists?

Thanks

Mike

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
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(256) 327-0966 (f)

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