LIMMA_analysis: Perform differential expression analysis using LIMMA

In mathiaskalxdorf/IceR: Requantification of label-free DDA proteomics data pre-analyzed by MaxQuant.

Perform differential expression analysis using LIMMA

Description

Perform differential expression analysis using LIMMA

Usage

LIMMA_analysis(
  data,
  assignments = NULL,
  batch = NULL,
  tech_reps = NULL,
  contrast = NULL
)

Arguments

data	Table of protein quantifications with samples in columns and features in rows.
assignments	Character vector of annotations of grouping per sample. By default set to NULL. In this case an ordinary one-sample test is performed.
batch	Optional character vector specifying sample batches.
tech_reps	Optional character vector specifying if samples are technical replicates
contrast	String of format Group1_vs_Group2 specifying contrast of interest. Replace Group1 and Group2 by groups specified in assignments.

Details

Perform differential expression analysis using R-package LIMMA.

Value

Returns a matrix which rows correspond to the proteins under analysis and columns indicate the corresponding abundance ratio, t-statistic, p-value and FDR adjusted p-value.

mathiaskalxdorf/IceR documentation built on Aug. 1, 2022, 8:03 a.m.