OLIN (version 1.50.0)

p.spatial2: Assessment of the significance of spatial bias based on p-values

Description

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.

Usage

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

Arguments

object

object of class marrayRaw or marrayNorm

delta

integer determining the size of spot neighbourhoods ((2*delta+1)x(2*delta+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.

Value

Pp) and negative (Pn) deviations of $median/mean of \code{M}$ of the spot's neighbourhood is produced (see example below).

Details

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.

See Also

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

Examples

# 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")