compareReplicateSD {RNAither} | R Documentation |
In the same fashion as spatialDistrib
, generates a plot of the standard deviation of replicate values.
compareReplicateSD(header, dataset, plotTitle, colname4SD, col4anno, showPlot)
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 |
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.
spatialDistrib
, compareReplicateSDPerScreen
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") compareReplicateSD(header, dataset, "Replicate standard intensity deviation", "SigIntensity", "GeneName", 1)