Why should I avoid technical replicates and pseudoreplicates?

When designing RNA-seq or ChIP-seq experiments, it is very important to avoid technical replicates and pseudo-biological replicates as they will lead to spurious results (e.g. spurious differential gene expression data; DGE data in case of RNA-seq).
Creating pseudo-biological replicates occurs frequently, especially for in vitro studies. Doing so can often lead to hundreds of false positive differentially expressed genes. For example, treating three cell-culture flasks of the same passage of a cell line as biological replicates would create such a dilemma.  Please see the excellent discussion of this topic by Christoph Emmerich here: https://paasp.net/accurate-design-of-in-vitro-experiments-why-does-it-matter/ .

This video by Josh Starmer explains why technical replicates are not helpful in principle in RNA-seq: https://www.youtube.com/watch?v=gKnfP2_Xdpo .

Category: 04 Library Preparation and QC

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