limma (version 3.28.6)

avedups: Average Over Duplicate Spots

Description

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

Usage

## S3 method for class 'default':
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.

Value

• A data object of the same class as x with 1/ndups as many rows.

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.

See Also

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