sigxy.plot2: Visualisation of significance tests for spatial bias
In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

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

This function produces a 2D-plot visualizing the significance of spatial bias.

1	sigxy.plot2(object,Sp,Sn,color.lim=c(-3,3),...)

`object`	object of class marrayRaw or marrayNorm
`Sp`	vector of false discovery rates or p-values for positive deviation of median/mean of \code{M} as produced by `fdrspatial` or `p.spatial`
`Sn`	vector of false discovery rate or p-values for negative deviation of median/mean of \code{M} as produced by `fdrspatial` or `p.spatial`
`color.lim`	limits of color range for plotting vector corresponding to log10(`pS`) and log10(`nS`)
`...`	Further optional graphical parameter for the `image` function generating the MXY plot

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

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

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

colorbar.sig, sigxy.plot, sigxy.plot,fdr.spatial2, p.spatial2, image

# To run these examples, "un-comment" them!
#
# LOADING DATA
# data(sw)
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# For this illustration, N was chosen rather small. For "real" analysis, it should be larger.
# FDR <- fdr.spatial2(sw,delta=2,N=10,av="median",edgeNA=TRUE)
#
# SIGNIFICANCE PLOTS OF ARRAY 1
# sigxy.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],color.lim=c(-5,5),main="FDR")
# SIGNIFICANCE PLOTS OF ARRAY 3
# sigxy.plot2(sw[,3],FDR$FDRp[[3]],FDR$FDRn[[3]],color.lim=c(-5,5),main="FDR")
#