makeBoxplotControlsPerPlate {RNAither} | R Documentation

## 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)

[Package RNAither version 2.38.0 Index]