replicatesCV {RNAither} | R Documentation

## Compute the correlation of variation (CV)

### Description

Computes the correlation of variation as defined in Tseng et al. (see References)

### Usage

    replicatesCV(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 to compute the correlation of variation
`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

The correlation of variation of an siRNA is defined as the standard deviation of its values divided by their mean.

The function generates a plot of the average intensity against the CV for each experiment. The plot will be saved as a pdf and a png file named after the experiment name specified in the header concatenated with the `PlotTitle`.

The function returns a list containing:

`histoName` | the plotname
`minOfScreens` | the number of the first experiment
`numOfScreens` | the number of the last experiment

### References

G. C. Tseng et al. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res, 29(12): 2549-2557, 2001.

### Examples

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

    replicatesCV(header, dataset, "Correlation of Variation versus Mean Intensity",
    "SigIntensity", "GeneName", 1, 0)

[Package RNAither version 2.28.0 Index]