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 2.28.0 Index]