channel2M: Convert Individual Channel Design Matrix to M-A Format
In limma: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	designI2M(design) designI2A(design)

design

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

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.

numeric model matrix with half as many rows as design

Gordon Smyth

model.matrix in the stats package.

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

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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)

     [,1] [,2] [,3]
[1,]    0    0    0
[2,]    0    0    0
[3,]    0    0    0
[4,]    0    0    0
     [,1] [,2] [,3]
[1,]    1    1    0
[2,]    1    1    0
[3,]    1    0    1
[4,]    1    0    1