modifyWeights: Modify Matrix of Weights By Control Status of Rows
In limma: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

Modify weights matrix for given gene status values.

1	modifyWeights(weights=rep(1,length(status)), status, values, multipliers)

`weights`	numeric matrix of relative weights, rows corresponding to genes and columns to arrays
`status`	character vector giving the control status of each spot on the array, of same length as the number of rows of `weights`
`values`	character vector giving subset of the unique values of `status`
`multipliers`	numeric vector of same length as `values` giving factor by which weights will be modified

The function is usually used to temporarily modify the weights matrix during normalization of data. The function can be used for example to give zero weight to spike-in ratio control spots during normalization.

Numeric matrix of same dimensions as weights with rows corresponding to values in status modified by the specified multipliers.

Gordon Smyth

An overview of normalization functions available in LIMMA is given in 05.Normalization.

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w <- matrix(runif(6*3),6,3)
status <- c("Gene","Gene","Ratio_Control","Ratio_Control","Gene","Gene")
modifyWeights(w,status,values="Ratio_Control",multipliers=0)