channel2M: Convert Individual Channel Design Matrix to M-A Format

In richierocks/limma2: Linear Models for Microarray Data

Description

Convert a design matrix in terms of individual channels to ones in terms of M-values or A-values for two-color microarray data.

Usage

designI2M(design)
designI2A(design)

Arguments

design

numeric model matrix with one row for each channel observation, i.e., twice as many rows as arrays

Details

If design is a model matrix suitable for modelling individual log-intensities for two color microarray data, then designI2M computes the corresponding model matrix for modelling M-values (log-ratios) and designI2A computes the model matrix for modelling A-values (average log-intensities).

Note that the matrices designI2M(design) or designI2A(design) may be singular if not all of the coefficients are estimable from the M or A-values. In that case there will be columns containing entirely zeros.

Value

numeric model matrix with half as many rows as design

Author(s)

Gordon Smyth

See Also

model.matrix in the stats package.

An overview of individual channel linear model functions in limma is given by 07.SingleChannel.

Examples

X <- cbind(1,c(1,1,1,1,0,0,0,0),c(0,0,0,0,1,1,1,1))
designI2M(X)
designI2A(X)

richierocks/limma2 documentation built on May 27, 2019, 8:47 a.m.