batch-effect-correction

1# Batch Effect Correction
2 
3## Prerequisites
4 
5Run the following before the first analysis to install all required R packages:
6 
7```bash
8Rscript -e "if (!require('BiocManager', quietly=TRUE)) install.packages('BiocManager'); BiocManager::install(c('sva', 'limma')); install.packages('ggplot2', repos='https://cloud.r-project.org')"
9```
10 
11> Note: `sva` and `limma` are Bioconductor packages and require `BiocManager` for installation. `ggplot2` is a standard CRAN package.
12 
13**The skill cannot run until these packages are installed.** In new or bare R environments, always run the prerequisite step first.
14 
15---
16 
17## When to Read External Files
18 
19| Situation | File to Read | Purpose |
20|-----------|--------------|---------|
21| **Need algorithm details** | `references/algorithm.md` | ComBat workflow, assumptions, and QC logic |
22| **Need to run analysis** | `scripts/main.R` | Execute: `Rscript scripts/main.R --input_file ... --group_file ...` |
23| **Encounter errors** | `references/troubleshooting.md` | Common errors and solutions |
24| **Need CLI examples** | `references/cli-guide.md` | Detailed CLI usage examples and baseline run record |
25| **Need test data** | `tests/data/` | Sample input files for testing |
26 
27---
28 
29## Usage
30 
31```bash
32Rscript scripts/main.R \
33  --input_file ./expression_matrix.csv \
34  --group_file ./sample_info.csv \
35  --output_dir ./output/ \
36  --batch_column batch \
37  --group_column group \
38  --sample_column sample \
39  --log_transform auto \
40  --timeout_seconds 600 \
41  --seed 42
42…