plateEffects {cellHTS2} | R Documentation

## Access plate effects stored in a cellHTS object.

### Description

This generic function accesses plate effects stored in slot `rowcol.effects` and `overall.effects` of a `cellHTS` instance.

### Usage

    plateEffects(object)

### Arguments

`object` | Object derived from class `cellHTS` that has been normalized by a spatial normalization method. See details.

### Value

`plateEffects` returns a list with two elements: `rowcol` and `overall`.
`plateEffects[["rowcol"]]` corresponds to the contents of slot `rowcol.effects` of `object`. This is a 3D array with the same dimensions as `Data(object)`: `nr of Features x nr of Samples x nr of Channels` of the current `cellHTS` object.
`plateEffects[["overall"]]` contains the data stored in slot `overall.effects` of `object`. This is a 3D array with dimensions `nr Plates x nr Samples x nr Channels` of `object`. Slot `overall.effects` is only estimated when B score method is used to normalize the data.
Note that these 2 slots accessed by this function were stored after preprocessing the data either using Bscore method or local regression fit (see `normalizePlates` for details), by setting the option `save.model=TRUE`.

### Author(s)

Ligia Bras ligia@ebi.ac.uk

### See Also

`cellHTS` `normalizePlates` `Bscore` `spatialNormalization`

[Package cellHTS2 version 2.2.5 Index]