arrayWeights {limma} | R Documentation

## Array Quality Weights

### Description

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

### Usage

    arrayWeights(object, design = NULL, weights = NULL, method = "genebygene", maxiter = 50, tol = 1e-10, trace=FALSE)
    arrayWeightsSimple(object, design = NULL, maxiter = 100, tol = 1e-6, maxratio = 100, trace=FALSE)

### Arguments

`object` | object of class `numeric`, `matrix`, `MAList`, `marrayNorm`, `ExpressionSet` or `PLMset` 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.
`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"`.
`maxiter` | maximum number of iterations allowed.
`tol` | convergence tolerance.
`maxratio` | maximum ratio between largest and smallest weights before iteration stops
`trace` | logical variable. If true then output diagnostic information at each iteration of '"reml"' algorithm.

### Details

The relative reliability of each array is estimated by measuring how well the expression values for that array follow the linear model.

The method is described in Ritchie et al (2006). 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 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 these array variances are converted to weights.

The data object `object` is interpreted as for `lmFit`. In particular, the arguments `design` and `weights` 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`.

`arrayWeightsSimple` is a fast version of `arrayWeights` with `method="reml"`, no prior weights and no missing values.

### Value

A vector of array weights.

### 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

    library(sma)
    # Subset of data from ApoAI case study in Limma User's Guide
    data(MouseArray)
    # Avoid non-positive intensities
    RG <- backgroundCorrect(mouse.data, method="half")
    MA <- normalizeWithinArrays(RG, mouse.setup)
    MA <- normalizeBetweenArrays(MA, method="Aq")
    targets <- data.frame(Cy3=I(rep("Pool",6)),Cy5=I(c("WT","WT","WT","KO","KO","KO")))
    design <- modelMatrix(targets, ref="Pool")
    arrayw <- arrayWeightsSimple(MA, design)
    fit <- lmFit(MA, design, weights=arrayw)
    fit2 <- contrasts.fit(fit, contrasts=c(-1,1))
    fit2 <- eBayes(fit2)
    # Use of array weights increases the significance of the top genes
    topTable(fit2)

[Package limma version 2.16.5 Index]