sigint.plot2: Visualisation of significance of intensity-dependent bias
In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Description Usage Arguments Details Note Author(s) See Also Examples

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

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

`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

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

This function will be merged with sigint.plot in future versions.

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

sigxy.plot, fdr.int2, p.int2

# 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