Perform limma differential expression on a ProtData object

This function takes a SummarizedExperiment object and two vectors containing the column names of the treatment and control samples. It filters out proteins found in fewer than 50% of samples, performs a limma-based differential expression analysis, and returns a data frame with metadata, intensities, log fold changes, and p-values.

Usage

do_limma(object, treatment_samples, control_samples)

Arguments

object

A SummarizedExperiment object containing protein intensities, metadata, and condition info.

treatment_samples

Character vector of column names representing treatment samples.

control_samples

Character vector of column names representing control samples.

Value

A data frame containing filtered proteins with metadata, intensity values, log fold change, p-value, and adjusted p-value.