Perform limma differential expression on a SummarizedExperiment

This function takes a SummarizedExperiment object and uses group labels in colData(object) to perform differential expression between a treatment group and a control group. Covariates can be included in the model design.

Usage

do_limma_binary(
  object,
  condition,
  treatment_group,
  control_group,
  covariates = NULL
)

Arguments

object

A SummarizedExperiment object containing protein intensities and metadata.

condition

String: column name in colData(object) that holds group labels.

treatment_group

String: name of treatment group in condition.

control_group

String: name of control group in condition.

covariates

Optional character vector: column names in colData(object) to use as covariates.

Value

A data frame with metadata, intensities, log fold change, p-values, and adjusted p-values.