avearrays {limma} | R Documentation

## Average Over Replicate Arrays

### Description

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

### Usage

    ## Default S3 method:
    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

`x` | a matrix-like object, usually a matrix, `MAList` or `EList` object.
`ID` | sample identifier.
`weights` | numeric matrix of non-negative weights

### 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.

### Value

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

### Author(s)

Gordon Smyth

### See Also

`avereps`.

02.Classes gives an overview of data classes used in LIMMA.

### Examples

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

[Package limma version 3.38.3 Index]