Batch Effect Correction

Prerequisites

Run the following before the first analysis to install all required R packages:

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.

When to Read External Files