bio-experimental-design-batch-design

Core Principle

Batch effects are unavoidable. Good design makes them correctable.

Design Rules

1. Never confound batch with condition - Each batch must contain all conditions
2. Balance samples across batches - Equal numbers per condition per batch
3. Randomize within constraints - Avoid systematic patterns
4. Include controls - Same samples across batches if possible

From count matrix

mod <- model.matrix(~condition, colData) mod0 <- model.matrix(~1, colData)