avearrays: Average Over Replicate Arrays

Description

Condense a microarray data object so that technical replicate arrays are replaced with (weighted) averages.

Usage

## S3 method for class 'default':
avearrays(x, ID=colnames(x), weights=NULL)
## S3 method for class 'MAList':
avearrays(x, ID=colnames(x), weights=x$weights)
## S3 method for class 'EList':
avearrays(x, ID=colnames(x), weights=x$weights)

Arguments

a matrix-like object, usually a matrix, MAList or EList object.

sample identifier.

weights

numeric matrix of non-negative weights

Value

A data object of the same class as x with a column for each unique value of ID.

Details

A new data object is computed in which technical replicate arrays are replaced by their (weighted) averages. For an MAList object, the components M and A are both averaged in this way, as are weights and any matrices found in object$other. EList objects are similar, except that the E component is averaged instead of M and A. If x is of mode "character", then the replicate values are assumed to be equal and the first is taken as the average.

Examples

Run this code

x <- matrix(rnorm(8*3),8,3)
colnames(x) <- c("a","a","b")
avearrays(x)