spatialNormalization: Spatial normalization
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

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

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.

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

`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.

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

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.

Ligia Bras ligia@ebi.ac.uk

medpolish, locfit, plotSpatialEffects, normalizePlates, summarizeChannels, plateEffects

    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)