Individual skill
batch-effect-correction
Use when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after QC plots. NOT for: single-cell integration, raw FASTQ processing, differential expression without batch labels, or datasets without biological groups.
awesome-med-research-skills/Data Analysis/batch-effect-correction/SKILL.md
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
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- engineering Derived category
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SKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 bytesSKILL.mdcore · 11,032 byteseval_report_batch-effect-correction_result.jsonasset · 12,419 bytesreferences/algorithm.mddoc · 3,739 bytesreferences/cli-guide.mddoc · 4,899 bytesreferences/troubleshooting.mddoc · 5,320 bytesscripts/functions.Rasset · 1,187 bytesscripts/input_functions.Rasset · 4,794 bytesscripts/main.Rruns · 4,429 bytesscripts/output_utils.Rasset · 1,855 bytesscripts/plotting.Rasset · 4,358 bytesscripts/run_analysis.Rasset · 1,225 bytesscripts/utils.Rasset · 3,937 bytestests/data/expression_matrix_merged.csvasset · 107,185 bytestests/data/sample_info.csvasset · 2,532 bytestests/run_tests.Rruns · 894 bytestests/testthat/helper-load-scripts.Rasset · 459 bytestests/testthat/setup.Rasset · 247 bytestests/testthat/test-batch-correction.Rasset · 6,520 bytes
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# Batch Effect Correction
## Prerequisites
Run the following before the first analysis to install all required R packages:
```bash
Rscript -e "if (!require('BiocManager', quietly=TRUE)) install.packages('BiocManager'); BiocManager::install(c('sva', 'limma')); install.packages('ggplot2', repos='https://cloud.r-project.org')"
```
> Note: `sva` and `limma` are Bioconductor packages and require `BiocManager` for installation. `ggplot2` is a standard CRAN package.
**The skill cannot run until these packages are installed.** In new or bare R environments, always run the prerequisite step first.
