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  • How many replicates in animal studies

    Dear All,
    Current guidelines (ENCODE, IHEC) for RNA-seq/ChIP-seq recommend at least two biological replicates, but it seems that these recommendations are based on studies from cell lines (e.g. Rozowsky et al, Nat. Biotech 2009). They aim at simple reproducibility checks, rather than proper variance estimates. Perhaps the development of more sophisticated variance models (e.g. DESeq) has also helped to keep the required number of replicates low.

    However, I could not find any references for animal/patient studies, where variability is much higher than for cell lines. More specifically I am interested in class comparison based on histone marks, but I'm concerned as other animal studies are often done for 10+ biological replicates.

    Does this forum have any expertise/suggestions?
    Thank you,
    Thomas

  • #2
    This doesn't help solve your question, but you may find it amusing . . .

    Biologist talks to statistician

    Comment


    • #3
      How many replicates in animal studies

      Rebecca Doerge and her group have done some work on this. You are correct in realizing two replicates is NOT enough.
      See

      Auer, P. L. and R. W. Doerge (2010). "Statistical design and analysis of RNA sequencing data." Genetics 185(2): 405-416.
      http://www.genetics.org/content/185/2/405.abstract

      Auer, P. L. and R. W. Doerge (2011). "A Two-Stage Poisson Model for Testing RNA-Seq Data." Statistical Applications in Genetics and Molecular Biology 10(1): 1-28.
      http://www.bepress.com/sagmb/vol10/iss1/art26/

      Those references should get you started.

      Comment

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