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Limma-based differential expression analysis for proteomics (unpaired)

Source: R/tools.R
limma_protein_DE.Rd

Limma-based differential expression analysis for proteomics (unpaired)

Usage

limma_protein_DE(
  expr,
  group,
  offset = NULL,
  contrast_str = NULL,
  trend = TRUE,
  robust = TRUE
)

Arguments

expr

Expression matrix.

group

Factor defining two groups to compare.

offset

Offset added before log2 transformation.

contrast_str

Contrast string for limma (e.g., "B-A").

trend

Whether to apply trend eBayes.

robust

Whether to apply robust eBayes.

Value

A data.frame containing logFC, P-values, adjusted P-values, mean log2 expression per group, and delta mean.