RNAither (version 2.20.0)

makeBoxplotControlsPerPlate: Generate a boxplot of the data vs. the controls for each plate

Description

Generates a boxplot of intensity values of negative controls, positive controls and experimental data for each plate of each experiment available in the dataset.

Usage

makeBoxplotControlsPerPlate(header, dataset, channel, plotTitle, plotDesign, showPlot)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

channel

a character string specifying the column whose values will be used for the boxplot

plotTitle

the plot title

plotDesign

1 or 2. 1 will generate one window containing all plots, 2 will generate a series of plots.

showPlot

0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows.

Value

For each experiment, a series of boxplots of intensity values of negative controls, positive controls and experimental data will be saved as a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle and the number of the experiment.The function returns a list containing:

plotName

the plotname

c(minOfScreens, numOfScreens)

a vector with the number of the first experiment and of the last experiment

c(minOfPlates, numOfPlates)

a vector with the number of the first plate and the number of the last plate

See Also

makeBoxplotControls, makeBoxplotControlsPerScreen, makeBoxplotPerPlate, makeBoxplotPerScreen

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

makeBoxplotControlsPerPlate(header, dataset, "SigIntensity", "Data vs. Controls", 1, 1)