compareReplicateSDPerScreen: Plot the standard deviation of replicates for each experiment

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

In the same fashion as spatialDistrib, generates plots of the standard deviation of replicate values for each experiment.

Usage

compareReplicateSDPerScreen(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 plots of the standard deviation of replicate values for each experiment. The plots are saved as png files named after the experiment name specified in the header concatenated with the plotTitle and the number of the experiment.

Wells showing positive controls sd are marked with a "P", wells showing negative controls sd with an "N".

The plots will also be saved as html files containing mouse-overs with the siRNA name for each well.

The function returns a list of length 3 containing:

basicPlotName	the plot name
minOfScreens	the number of the first experiment
numOfScreens	the number of the last experiment

See Also

spatialDistrib, compareReplicateSD

Examples

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

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

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.