p.spatial2: Assessment of the significance of spatial bias based on...
In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

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

This function assesses the significance of spatial bias. This is achieved by comparing the observed average values of logged fold-changes within a spot's spatial neighbourhood with an empirical distribution generated by permutation tests. The significance is given by (adjusted) p-values derived in one-sided permutation test.

1	p.spatial2(object,delta=2,N=-1,av="median",p.adjust.method="none")

`object`	object of class marrayRaw or marrayNorm
`delta`	integer determining the size of spot neighbourhoods (`(2delta+1)x(2delta+1)`).
`N`	number of samples for generation of empirical background distribution
`av`	averaging of `M` within neighbourhood by mean or median (default)
`p.adjust.method`	method for adjusting p-values due to multiple testing regime. The available methods are “none”, “bonferroni”, “holm”, “hochberg”, “hommel” and “fdr”. See also `p.adjust`.

The function p.spatial2.Rd is basically the same as p.spatial, but differs in its input and output formats. Details about the functionality can be found at p.spatial.

A list of a two lists of vectors is produced containing the p-values for positive (Pp) and negative (Pn) deviations of median/mean of \code{M} of the spot's neighbourhood is produced (see example below).

This function will be fused with p.spatial in future versions using S4-style methods.

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

fdr.int, sigxy.plot, p.adjust,p.spatial

# 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.
# P <- p.spatial2(sw,delta=2,N=10000,av="median")
# SIGNIFICANCE PLOTS OF ARRAY 1
# sigxy.plot2(sw[,1],P$Pp[[1]],P$Pn[[1]],color.lim=c(-5,5),main="P-value")
# SIGNIFICANCE PLOTS OF ARRAY 3
# sigxy.plot2(sw[,3],P$Pp[[3]],P$Pn[[3]],color.lim=c(-5,5),main="P-value")