avereps {limma} | R Documentation

## Average Over Irregular Replicate Probes

### Description

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

### Usage

    ## Default S3 method:
    avereps(x, ID=rownames(x), ...)
    ## S3 method for class 'MAList'
    avereps(x, ID=NULL, ...)
    ## S3 method for class 'EList'
    avereps(x, ID=NULL, ...)

### Arguments

`x` | a matrix-like object, usually a matrix, `MAList` or `EList` object.
`ID` | probe identifier.
`...` | other arguments are not currently used.

### Details

A new data object is computed in which each probe ID is represented by the average of its replicate spots or features.

For an `MAList` object, the components `M` and `A` are both averaged in this way, as are `weights` and any matrices found in `object$other`. For an `MAList` object, `ID` defaults to `MA$genes$ID` is that exists, otherwise to `rownames(MA$M)`.

`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 row for each unique value of `ID`.

### Note

This function should only be applied to normalized log-expression values, and not to raw unlogged expression values. It will generate an error message if applied to `RGList` or `EListRaw` objects.

### Author(s)

Gordon Smyth

### See Also

`avedups`, `avearrays`. Also `rowsum` in the base package.

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

### Examples

    x <- matrix(rnorm(8*3),8,3)
    colnames(x) <- c("S1","S2","S3")
    rownames(x) <- c("b","a","a","c","c","b","b","b")
    avereps(x)

[Package limma version 3.50.3 Index]