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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
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
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