Topic
Batch effects
Is a batch effect confounding my comparison, and should I correct it?
Batch effects are technical variation from processing date, library prep, sequencing lane or operator that shows up as a dominant axis in PCA. Whether to correct depends entirely on whether batch is confounded with the biological condition; if it is, no method can separate them and the honest answer is a redesign.
- 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.
- How to Detect Batch Effects in Single-Cell ATAC-seq
Your LSI plot separates by processing date instead of cell type, here's the order of checks that tells you whether that's a fixable artifact or a confound no tool can undo.
- How to Detect Batch Effects in Single-Cell RNA-seq
Before you pick Harmony, RPCA or scVI, find out whether batch is separable from your condition at all, because no method fixes a confounded design.
- How to Detect Batch Effects in Single-Nucleus RNA-seq
Before you run Harmony on your frozen-tissue nuclei, find out whether the batch axis is technical noise or the condition you came to study.
- How to Detect Batch Effects in Spatial Transcriptomics
A slide is not a replicate, learn to tell tissue-section artifact from real biology before you trust a single cluster.