adjustFluo: adjustFluo

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

It performs the run effect correction and normalization of the raw fluorescence signals.

Usage

adjustFluo(data, transformation, BGmethod, maxMix, reference, prior.pi,
  flex.reps, flexmethod, image.type, savePlot, seed, dateIndex)

Arguments

data	List. A list with the fluorescence signal information of both channels.
BGmethod	Character string. The type of image background correction to be performed. One of "normexp" or "subtract".
maxMix	Integer. The maximum number of components to fit into the mixture of regressions model. If maxMix=1 or if the the optimal number of the estimated components is 1, the model reduces to the classical 2-way ANOVA.
reference	Numeric vector. Specifies the runs to be used as baseline (iteratively).
prior.pi	Float. The prior probability to accept a component.
flex.reps	Integer. The iterations of the Expectation-Maximization algorithm to estimate the flexmix model.
flexmethod	Character string. A method to estimate the optimal number of flexmix components. One of "BIC", "AIC", "ICL".
image.type	Character string. A triplet of IDs to characterize the type of images under study.
savePlot	Character string. The directory to store the plots or an option to print them on the screen.
seed	Integer. An optional seed number for the Random Number Generator.
dateIndex	Character string. a date index to be used in saving the output files.
transform	Character string. The type of transformation to be performed. One of "bc" (Box-Cox), "log", "log10" or "asinh".

Value

A list with the fluorescence signals, mixture components and flexmix model estimates

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.