expressionMatrixToMvalue: Turn a matrix of Gene Expression into M-values

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Turn a matrix of Gene Expression into M-values

Description

Translate raw gene abundance data into log2 fold change data commonly called M-values

Usage

expressionMatrixToMvalue(x, average.FUN = median, minIntensity = 0, small.offset = 1)

Arguments

x	Matrix of gene expression data, as form expressionFileSetToMatrix
average.FUN	The averaging function to apply to each row of m, to get the denominator for dividing the row elements
minIntensity	The minimum allowed value for elements of m, to put a floor on low expression values
small.offset	The linear offset to add to all row elements, before division and log2 transform, to prevent divide-by-zero results and to minimize extreme fold changes from very low expression values

Details

After M-value transformation, those row elements that are greater than the average expression will be positive, while elements lower than the average expression will be negative values. A value of 1.0 means 2-fold higher expression and a value of -2.0 means 4-fold lower expression.

Value

A matrix of M-value fold change data, of the same dimensions and names as m, suitable for heatmaps, etc.

Note

This function is called by 'expressionHeatmap()'

robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.