generateE {beadarray} | R Documentation

## Generate Error Image for BeadLevelList object

### Description

Generates an Error Image from the data in a `BeadLevelList` object.

### Usage

    generateE(BLData, array, neighbours = NULL, log = TRUE, method = "median", what = "residG", bgfilter = "none", invasions = 20)

### Arguments

`BLData` | `BeadLevelList`
`array` | integer specifying which strip/array to plot
`neighbours` | A Neighbours matrix. Optional - if left NULL, it will be computed.
`log` | Logical. If TRUE, compute residuals on the log scale.
`method` | Method for computing residuals. Options are `"mean"` and `"median"`
`what` | What to derive the error image from, as used in `getArrayData`.
`bgfilter` | Method passed to the function `BGFilter`. Options are "none", "mean", "median", "MAD" and "medianMAD".
`invasions` | Integer - Number of invasions. This argument is passed to the function BGfilter.

### Details

generateE creates an error image, usually based on bead residuals. This output can then be fed into `BASHDiffuse` or `BASHExtended`.

If `what` is `residG`, `residR`, or `residM`, then residuals are calculated based on `method`. For other values of `what`, the residuals are not calculated.

We then apply a "background filter" to this data, using the function `BGFilter` with arguments `bgfilter` and `invasions` - see its help file for more details. The background filter subtracts an estimate of the local background of the error image, and/or scales by the local MAD. This step is disabled by using `bgfilter = "none"`.

### Value

An "Error Image" - a vector of length equal to the number of beads on the array.

### Author(s)

Jonathan Cairns

### See Also

`BGFilter`

### Examples

    data(BLData)
    E <- generateE(BLData,1)
    E <- generateE(BLData,1, invasions = 10) #reduced no of invasions to increase speed.
    E <- generateE(BLData,1, bgfilter = "none") #residuals (median)

[Package beadarray version 1.12.1 Index]