RNAither (version 2.20.0)

compareReplicateSD: Plot the standard deviation of replicates

Description

In the same fashion as spatialDistrib, generates a plot of the standard deviation of replicate values.

Usage

compareReplicateSD(header, dataset, plotTitle, colname4SD, col4anno, showPlot)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

plotTitle

the plot title

colname4SD

a character string specifying the column whose values will be used for the computation of the replicate standard deviation

col4anno

a character string specifying the name of the dataset column to be used to define the replicate, e.g. "GeneName" or "Internal_GeneID"

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

Generates a plot of the standard deviation of replicate values of all experiments. The plot is saved as a png file named after the experiment name specified in the header concatenated with the plotTitle.Wells showing positive controls sd are marked with a "P", wells showing negative controls sd with an "N".The plot will also be saved as an html file containing mouse-overs with the siRNA name for each well.The function returns the plotname.

See Also

spatialDistrib, compareReplicateSDPerScreen

Examples

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

compareReplicateSD(header, dataset, "Replicate standard intensity deviation", 
"SigIntensity", "GeneName", 1)