replicatesCV {RNAither} | R Documentation |
Computes the correlation of variation as defined in Tseng et al. (see References)
replicatesCV(header, dataset, PlotTitle, col4val, col4anno, plotDesign, showPlot)
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 to compute the correlation of variation |
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. |
The correlation of variation of an siRNA is defined as the standard deviation of its values divided by their mean.
The function generates a plot of the average intensity against the CV for each experiment. The plot will be saved as a pdf and a png file named after the experiment name specified in the header concatenated with the PlotTitle
.
The function returns a list containing:
histoName |
the plotname |
minOfScreens |
the number of the first experiment |
numOfScreens |
the number of the last experiment |
G. C. Tseng et al. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res, 29(12): 2549-2557, 2001.
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") replicatesCV(header, dataset, "Correlation of Variation versus Mean Intensity", "SigIntensity", "GeneName", 1, 0)