Guides
Sanity checks, by assay
Each guide answers one question about one kind of data: what the failure looks like, why it happens, the checks that expose it, and when leaving it alone is the right call.
Bulk RNA-seq
- How to Detect Batch Effects in Bulk RNA-seq
A PCA plot that separates by prep date instead of treatment is telling you the truth about your experiment, not a bug to plot around.