compareReplicates {RNAither} | R Documentation

## Compare replicate values

### Description

Plots replicate intensities pairwise for each experiment.

### Usage

    compareReplicates(header, dataset, plotTitle, col4val, col4anno, plotDesign, showPlot)

### Arguments

`header` | the header of a dataset file generated with `generateDatasetFile`
`dataset` | an R data frame generated with `generateDatasetFile`
`plotTitle` | the plot title
`col4val` | a character string specifying the column whose values will be used for the plot
`col4anno` | a character string specifying the name of the dataset column to be used to define the replicate, e.g. `"GeneName"` or `"Internal_GeneID"`
`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, plots of pairwise comparisons between replicate intensities are generated and 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 plot name
`minOfScreens` | the number of the first experiment
`numOfScreens` | the number of the last experiment
`maxCombinationNum` | the number of replicates to compare

### See Also

`compareReplicaPlates`

### Examples

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

    compareReplicates(header, dataset, "Comparison of Replicates", "SigIntensity", "GeneName", 1, 0)

[Package RNAither version 2.28.0 Index]