limma (version 3.28.14)

modifyWeights: Modify Matrix of Weights By Control Status of Rows

Description

Modify weights matrix for given gene status values.

Usage

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

Arguments

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

Value

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

Details

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.

See Also

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

Examples

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)