avearrays: Average Over Replicate Arrays
In limma: Linear Models for Microarray Data

Description Usage Arguments Details Value Author(s) See Also Examples

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

## 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)

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

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.

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

Gordon Smyth

avereps.

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

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

               a          b
[1,]  0.06818442  0.1725134
[2,]  0.39106518  1.6426725
[3,] -0.74722260  0.3671410
[4,]  0.71964981 -0.3534182
[5,]  0.63591556  0.1816293
[6,] -0.44054880 -0.2362331
[7,] -0.11815876  1.1829985
[8,] -0.24357897 -1.0567411