avedups {limma} | R Documentation

## Average Over Duplicate Spots

### Description

Condense a microarray data object so that values for within-array replicate spots are replaced with their average.

### Usage

    ## Default S3 method:
    avedups(x, ndups=2, spacing=1, weights=NULL)
    ## S3 method for class 'MAList'
    avedups(x, ndups=x$printer$ndups, spacing=x$printer$spacing, weights=x$weights)
    ## S3 method for class 'EList'
    avedups(x, ndups=x$printer$ndups, spacing=x$printer$spacing, weights=x$weights)

### Arguments

`x` | a matrix-like object, usually a matrix, `MAList` or `EList` object.
`ndups` | number of within-array replicates for each probe.
`spacing` | number of spots to step from a probe to its duplicate.
`weights` | numeric matrix of spot weights.

### Details

A new data object is computed in which each probe is represented by the (weighted) average of its duplicate spots. For an `MAList` object, the components `M` and `A` are both averaged in this way. For an `EList` object, the component `E` is averaged in this way.

If `x` is of mode `"character"`, then the duplicate 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 `1/ndups` as many rows.

### Author(s)

Gordon Smyth

### See Also

`avereps`.

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

[Package limma version 3.42.2 Index]