gls.series {limma}R Documentation

Fit Linear Model to Microarray Data by Generalized Least Squares

Description

Fit a linear model genewise to expression data from a series of microarrays. The fit is by generalized least squares allowing for correlation between duplicate spots or related arrays. This is a utility function for lmFit.

Usage

gls.series(M,design=NULL,ndups=2,spacing=1,block=NULL,correlation=NULL,weights=NULL,...)

Arguments

M numeric matrix containing log-ratio or log-expression values for a series of microarrays, rows correspond to genes and columns to arrays.
design numeric design matrix defining the linear model, with rows corresponding to arrays and columns to comparisons to be estimated. The number of rows must match the number of columns of M. Defaults to the unit vector meaning that the arrays are treated as replicates.
ndups positive integer giving the number of times each gene is printed on an array. nrow(M) must be divisible by ndups.
spacing the spacing between the rows of M corresponding to duplicate spots, spacing=1 for consecutive spots
block vector or factor specifying a blocking variable on the arrays. Same length as ncol(M).
correlation numeric value specifying the inter-duplicate or inter-block correlation.
weights an optional numeric matrix of the same dimension as M containing weights for each spot. If it is of different dimension to M, it will be filled out to the same size.
... other optional arguments to be passed to dupcor.series.

Details

This is a utility function used by the higher level function lmFit. Most users should not use this function directly but should use lmFit instead.

This function is for fitting gene-wise linear models when some of the expression values are correlated. The correlated groups may arise from replicate spots on the same array (duplicate spots) or from a biological or technical replicate grouping of the arrays. This function is normally called by lmFit and is not normally called directly by users.

Note that the correlation is assumed to be constant across genes. If correlation=NULL then a call is made to duplicateCorrelation to estimated the correlation.

Value

A list with components

coefficients numeric matrix containing the estimated coefficients for each linear model. Same number of rows as M, same number of columns as design.
stdev.unscaled numeric matrix conformal with coef containing the unscaled standard deviations for the coefficient estimators. The standard errors are given by stdev.unscaled * sigma.
sigma numeric vector containing the residual standard deviation for each gene.
df.residual numeric vector giving the degrees of freedom corresponding to sigma
correlation inter-duplicate or inter-block correlation
qr QR decomposition of the generalized linear squares problem, i.e., the decomposition of design standardized by the Choleski-root of the correlation matrix defined by correlation

Author(s)

Gordon Smyth

See Also

duplicateCorrelation.

An overview of linear model functions in limma is given by 06.LinearModels.


[Package limma version 2.4.7 Index]