Xprep {SAGx}R Documentation

Calculation of input to stat.bayesian starting from linear model

Description

The function fits a linear model to a microarray data matrix.

Usage

Xprep(indata=M, formula=~as.factor(g), contrast=c(0,1), design=NULL,Vars=NULL)

Arguments

indata The data matrix
formula a linear model formula in the lm format
contrast a vector defining the contrast of interest
design the design matrix
Vars if not null the variance of the se is estimated through jacknife.

Details

As of v1.5 the code has been improved in terms of speed and takes advantage of built-in R functions. This incereases the efficiency of e.g. samroc.

Value

a list with the entries

Mbar estimate of the contrast
Vest the error variance
k inverse of the scale factor turning Vest into a standard error
f the degrees of freedom of Vest
design the design matrix
Varse The variance of the standard error

Author(s)

Per Broberg


[Package SAGx version 1.6.0 Index]