RNAither (version 2.20.0)

replicatesCV: 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)