limmaRatioDE: Simple one-sample differential expression with limma

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Simple one-sample differential expression with limma

Description

limmaDE is a wrapper around limma to perform a differential expression for one condition against the null hypothesis of one. This is designed to be used with SILAC ratios.

Usage

limmaRatioDE(pdat, condition = NULL, transform.fun = log2, sig.level = 0.05)

Arguments

pdat	Protein proteusData object.
condition	Condition name.
transform.fun	A function to transform data before differential expression.
sig.level	Significance level for rejecting the null hypothesis.

Details

Performs differential expression for one condition, assuming the measured values are ratios and the null hypothesis is the ratio of 1. The analysis is done in logarithmic space, so the actual null hypothesis tested is log ratio = 0. The log fold change returned is the log mean ratio of the condition.

Before limma is called, intensity data are transformed using the transform.fun function. The default for this transformation is log2. Therefore, by default, the column "logFC" in the output data frame contains log2 fold change. If you need log10-based fold change, you can use transform.fun=log10.

limmaDE is only a simple wrapper around limma, to perform differential expression between two conditions. For more complicated designs we recommend using limma functions directly.

Value

A data frame with DE results. "logFC" column is a log-fold-change (using the transform.fun). Attributes contain additional information about the transformation function, significance level and condition name.

Examples

## Not run: 
library(proteusSILAC)
data(proteusSILAC)
prodat.norm <- normalizeData(prodat)
res <- limmaRatioDE(prodat.norm, condition="T48")

## End(Not run)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.