fdr.spatial2: Assessment of the significance of spatial bias
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 by a one-sided random permutation test. 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 random permutation. The significance of spatial bias is given by the false discovery rate.

1	fdr.spatial2(object,delta=2,N=100,av="median",edgeNA=FALSE)

`object`	object of class marrayRaw or marrayNorm
`delta`	integer determining the size of spot neighbourhoods (`(2delta+1)x(2delta+1)`).
`N`	number of random permutations performed for generation of empirical background distribution
`av`	averaging of `M` within neighbourhood by mean or median (default)
`edgeNA`	treatment of edges of array: For `edgeNA=TRUE`, the significance of a neighbourhood (defined by a sliding window) is set to NA, if the neighbourhood extends over the edges of the matrix.

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

Two list of vectors containing the false discovery rates for positive (FDRp) and negative (FDRn) deviations of median/mean of \code{M} of the spot's neighbourhood is produced. Each vector contains the false discovery values for one array.

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

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

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

# To run these examples, delete the comment signs before the commands.
#
# 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")
#