makeBoxplotControlsPerPlate: Generate a boxplot of the data vs. the controls for each...
In RNAither: Statistical analysis of high-throughput RNAi screens

Description Usage Arguments Value See Also Examples

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

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

`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.

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

makeBoxplotControls, makeBoxplotControlsPerScreen, makeBoxplotPerPlate, makeBoxplotPerScreen

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

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