normalize-SynergyScreen-method: Normalize synergy screen data

In ybukhman/SynergyScreen: Analyze and simulate synergy screen data

Description

Normalization corrects for plate bias and subtracts blank response

Usage

## S4 method for signature 'SynergyScreen'
normalize(object, floor = 0.001)

Arguments

object	object of class SynergyScreen
floor	numeric, normalized non-blank response values smaller than this number are set to this number

Details

Normalization assumes that there is a multiplicative plate bias. A bias factor is computed for each plate based on untreated control response values. A plate's bias is its mean divided by the global mean. To normalize, all response values in a plate are divided by the plate's bias factor.

Value

object of class SynergyScreen with populated @norm_data slot and @response and @control.response slots of @dre_list members

See Also

SynergyScreen, BiocGenerics::normalize

Examples

# Initialize a screen
cpds <- readCompoundFile(system.file("extdata/15_cpds_simulation/compounds_1.csv",
                                    package="SynergyScreen"))
screen1 <- new("SynergyScreen",compound_list=cpds)
screen1 <- generateDesign(screen1,pairs=FALSE)

#  Simulate compound growth curve characteristics and raw dose-response data
set.seed(20141120)
screen1 <- simulate(screen1)
boxplot(screen1,"raw")

#  Normalize screen data, adjusting for plate bias
screen1 <- normalize(screen1)
boxplot(screen1,"norm")

ybukhman/SynergyScreen documentation built on May 4, 2019, 2:31 p.m.