lmFit {limma}R Documentation

Linear Model for Series of Arrays

Description

Fit linear model for each gene given a series of arrays

Usage

lmFit(object,design=NULL,ndups=1,spacing=1,correlation=0.75,weights=NULL,method="ls",...) 

Arguments

object object of class numeric, matrix, MAList, marrayNorm or exprSet containing log-ratios or log-values of expression for a series of microarrays
design the design matrix of the microarray experiment, with rows corresponding to arrays and columns to coefficients to be estimated. Defaults to the unit vector meaning that the arrays are treated as replicates.
ndups a positive integer giving the number of times each gene is printed on an array
spacing the spacing between duplicate spots, spacing=1 for consecutive spots
correlation the inter-duplicate correlation
weights an optional numeric matrix containing weights for each spot
method character string, "ls" for least squares or "robust" for robust regression
... other optional arguments to be passed to lm.series, gls.series or rlm.series

Details

A linear model is fitted for each gene by calling one of lm.series, gls.series or rlm.series. Note that the arguments design, ndups will be extracted from the data object if available and do not normally need to set explicitly in the call. If arguments are set in the call then they will over-ride slots or components in the data object.

Value

Object of class MArrayLM

Author(s)

Gordon Smyth

See Also

An overview of linear model functions in limma is given by 5.LinearModels.


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