spatialNormalization {cellHTS2} | R Documentation

## Spatial normalization

### Description

Adjust spatial plate effects. This function works on the data stored in the slot `assayData` of a `cellHTS` object by fitting a bivariate function within each plate using local regression (`robust local fit`) with second degree polynomials. Only wells containing `"sample"` are considered for the parameter fitting, but adjusted data for all wells are returned.

### Usage

    spatialNormalization(object, save.model=FALSE, ...)

### Arguments

`object` | a `cellHTS` object that has already been configured.
`...` | Parameters that get passed on to the `lp` function of `locfit`. Most relevant are `nn` and `h`.
`save.model` | a logical value specifying whether the values of the fitted adjustment functions should be returned in the slot `rowcol.effects` of the returned object.

### Details

This function is typically not called directly, but rather indirectly from `normalizePlates` function. The normalization is performed separately for each replicate and channel.

### Value

An object of class `cellHTS` with normalized data stored in slot `assayData`. Furthermore, if `save.model=TRUE`, it will contain a slot `rowcol.effects`, a 3D array with the same dimension as `Data(object)`.

Moreover, the processing status of the `cellHTS` object is updated in the slot `state` to `object@state[["normalized"]]=TRUE`.

### Author(s)

Ligia Bras ligia@ebi.ac.uk

### See Also

`medpolish`, `locfit`, `plotSpatialEffects`, `normalizePlates`, `summarizeChannels`, `plateEffects`

### Examples

        data(KcViabSmall)
        x <- KcViabSmall
        xs <- spatialNormalization(x, save.model = TRUE, h=3)

        ## Calling spatialNormalization function from "normalizePlates":
        xopt <- normalizePlates(x, varianceAdjust="none", save.model = TRUE, method="locfit", h=3)
        all(xs@rowcol.effects == xopt@rowcol.effects)

[Package cellHTS2 version 2.52.0 Index]