/bio-experimental-design-batch-design

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--- name: bio-experimental-design-batch-design description: Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals. tool_type: r primary_tool: sva measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

• read_file
• run_shell_command

---

Batch Design and Mitigation

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

Balanced Design Example

# BAD: Confounded design
# Batch 1: All treated samples
# Batch 2: All control samples
# -> Cannot separate batch from treatment

# GOOD: Balanced design
# Batch 1: 3 treated, 3 control
# Batch 2: 3 treated, 3 control
# -> Batch effect can be estimated and removed

Sample Assignment

library(designit)

# Create balanced assignment
samples <- data.frame(
  sample_id = paste0('S', 1:24),
  condition = rep(c('ctrl', 'treat'), each = 12),
  sex = rep(c('M', 'F'), 12)
)

# Optimize batch assignment
batch_design <- osat(samples, batch_size = 8,
                     balance_cols = c('condition', 'sex'))

Detecting Batch Effects

library(sva)

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

# Estimate number of surrogate variables (hidden batches)
n_sv <- num.sv(counts_normalized, mod)

# Estimate surrogate variables
svobj <- sva(counts_normalized, mod, mod0, n.sv = n_sv)

Correction Methods

| Method | When to Use | |--------|-------------| | ComBat | Known batches, moderate effects | | SVA | Unknown batches, exploratory | | RUVseq | Using control genes | | limma::removeBatchEffect | Visualization only |

Documenting Design

Always record:

• Date of sample processing
• Reagent lot numbers
• Operator
• Equipment/lane assignments
• Any deviations from protocol

Related Skills

• experimental-design/power-analysis - Account for batch in power calculations
• differential-expression/batch-correction - Correcting batch effects in analysis
• single-cell/batch-integration - scRNA-seq batch correction

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