repMeans: Compute mean of replicated spots
In MKomics: Omics Data Analysis

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

Compute mean of replicated spots where additionally spot flags may incorporated.

1	repMeans(x, flags, use.flags = NULL, ndups, spacing, method, ...)

`x`	matrix or data.frame of expression values
`flags`	matrix or data.frame of spot flags; must have same dimension as `x`
`use.flags`	should flags be included and in which way; cf. section details
`ndups`	integer, number of replicates on chip. The number of rows of `x` must be divisible by `ndups`
`spacing`	the spacing between the rows of 'x' corresponding to replicated spots, `spacing = 1` for consecutive spots; cf. function `unwrapdups` in package `"limma"`
`method`	function to aggregate the replicated spots. If missing, the mean is used.
`...`	optional arguments to `method`.

The incorporation of spot flags is controlled via argument use.flags.

NULL: flags are not used; minimum flag value of replicated spots is returned

"max": only spots with flag value equal to the maximum flag value of replicated spots are used

"median": only spots with flag values larger or equal to median of replicated spots are used

"mean": only spots with flag values larger or equal to mean of replicated spots are used

LIST with components

`exprs`	mean of expression values
`flags`	flags for mean expression values

A first version of this function appeared in package SLmisc.

Matthias Kohl Matthias.Kohl@stamats.de

unwrapdups

## only a dummy example
M <- matrix(rnorm(1000), ncol = 10)
FL <- matrix(rpois(1000, lambda = 10), ncol = 10) # only for this example
res <- repMeans(x = M, flags = FL, use.flags = "max", ndups = 5, spacing = 20)