RNAither (version 2.20.0)

compareReplicates: 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)