compareReplicateSD {RNAither}R Documentation

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)

[Package RNAither version 1.4.6 Index]