printtipWeights: Sub-array Quality Weights

In richierocks/limma2: Linear Models for Microarray Data

Description

Estimates relative quality weights for each sub-array in a multi-array experiment.

Usage

printtipWeights(object, design = NULL, weights = NULL, method = "genebygene", layout, maxiter = 50, tol = 1e-10, trace=FALSE)

Arguments

object	object of class numeric, matrix, MAList, marrayNorm, or ExpressionSet containing log-ratios or log-values of expression for a series of spotted 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.
weights	optional numeric matrix containing prior weights for each spot.
method	character string specifying the estimating algorithm to be used. Choices are "genebygene" and "reml".
layout	list specifying the dimensions of the spot matrix and the grid matrix. For details see PrintLayout-class.
maxiter	maximum number of iterations allowed.
tol	convergence tolerance.
trace	logical variable. If true then output diagnostic information at each iteration of '"reml"' algorithm.

Details

The relative reliability of each sub-array (print-tip group) is estimated by measuring how well the expression values for that sub-array follow the linear model.

The method described in Ritchie et al (2006) and implemented in the arrayWeights function is adapted for this purpose. A heteroscedastic model is fitted to the expression values for each gene by calling the function lm.wfit. The dispersion model is fitted to the squared residuals from the mean fit, and is set up to have sub-array specific coefficients, which are updated in either full REML scoring iterations, or using an efficient gene-by-gene update algorithm. The final estimates of the sub-array variances are converted to weights.

The data object object is interpreted as for lmFit. In particular, the arguments design, weights and layout will be extracted from the data object if available and do not normally need to be set explicitly in the call; if any of these are set in the call then they will over-ride the slots or components in the data object.

Value

A matrix of sub-array weights which can be passed to lmFit.

Author(s)

Matthew Ritchie and Gordon Smyth

References

Ritchie, M. E., Diyagama, D., Neilson, van Laar, R., J., Dobrovic, A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights in the analysis of microarray data. BMC Bioinformatics 7, 261. http://www.biomedcentral.com/1471-2105/7/261/abstract

See Also

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

Examples

## Not run: 
# This example is designed for work on a subset of the data
# from ApoAI case study in Limma User's Guide

RG <- backgroundCorrect(RG, method="normexp")
MA <- normalizeWithinArrays(RG)
targets <- data.frame(Cy3=I(rep("Pool",6)),Cy5=I(c("WT","WT","WT","KO","KO","KO")))
design <- modelMatrix(targets, ref="Pool")
subarrayw <- printtipWeights(MA, design, layout=mouse.setup)
fit <- lmFit(MA, design, weights=subarrayw)
fit2 <- contrasts.fit(fit, contrasts=c(-1,1))
fit2 <- eBayes(fit2)
# Use of sub-array weights increases the significance of the top genes
topTable(fit2)
# Create an image plot of sub-array weights from each array
zlim <- c(min(subarrayw), max(subarrayw))
par(mfrow=c(3,2), mai=c(0.1,0.1,0.3,0.1))
for(i in 1:6) 
	imageplot(subarrayw[,i], layout=mouse.setup, zlim=zlim, main=paste("Array", i))

## End(Not run)

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