OLIN (version 1.50.0)

sigint.plot2: Visualisation of significance of intensity-dependent bias

Description

This function produce visualises the significance of intensity-dependent bias.

Usage

sigint.plot2(object,Sp,Sn,ylim=c(-3,-3),...)

Arguments

object

object of class marrayRaw or marrayNorm

Sp

vector of false discovery rate or p-values for positive deviation of $median/mean of \code{M}$ as produced by fdr.int2 or p.int2

Sn

vector of false discovery rate or p-values for negative deviation of $median/mean of \code{M}$ as produced by fdr.int2 or p.int2

ylim

vector of minimal log10(fdr) or log10(p-value) to be visualised corresponding to Sp and Sn. FDR or p-values smaller than these values will be set equal to these threshold values for visualisation.

...

Further optional graphical parameter for the plot function generating the MA plot

Details

The function sigint.plot2 only differs from sigint.plot in its input arguments. The functionality is the same. For details, see sigint.plot.

See Also

sigxy.plot, fdr.int2, p.int2

Examples

# To run these examples, delete the comment signs (#) in front of the commands.
#
# LOADING DATA NOT-NORMALISED
# data(sw)
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# For this example, N was chosen rather small. For "real" analysis, it should be larger.
# FDR <- fdr.int2(sw,delta=50,N=10,av="median")
# VISUALISATION OF RESULTS
# sigint.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],c(-5,-5)) # array 1
# sigint.plot2(sw[,4],FDR$FDRp[[4]],FDR$FDRn[[4]],c(-5,-5)) # array 4