Topic
Outlier samples in PCA
One sample sits far from the others in PCA; do I drop it?
An outlier in PCA is a question, not a verdict: it may be a failed library, a swap, a different tissue region, or the most interesting sample you have. The decision requires QC metrics and metadata, and dropping samples to make a result significant is p-hacking with extra steps.
- How to Handle Outlier Samples in PCA in Bulk RNA-seq
PCA can't tell you whether a stray point is a dead library or your best result; your QC metrics and metadata have to do that job for it.