sig.mask: Masking of data based on significance testing

In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Description

This function sets data to NA if the corresponding spots have significantly biased neighbourhoods on the intensity scale or on the spatial dimensions of the array.

Usage

sig.mask(object,Sp,Sn,thrp,thrn) 

Arguments

object	object of class marrayRaw or marrrayNorm
Sp	list of vectors of false discovery rate or p-values for positive deviation of median/mean of \code{M} as produced by fdr.int2, p.int2, fdr.spatial2 or p.spatial2.
Sn	list vector of false discovery rate or p-values for negative deviation of median/mean of \code{M} as produced by fdr.int2, p.int2, fdr.spatial2 or p.spatial2.
thrp	vector of thresholds for significance of positive deviation (Sp)
thrn	vector of thresholds for significance of negative deviation (Sn)

Details

This function can be used for the masking of data that has been decided to be unrelaible after the application of significance test for intenstiy- and location dependent dye bias (e.g. p.int2, fdr.int2, p.spatial2, fdr.spatial2).

Author(s)

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

See Also

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

Examples

# To run these commands, delete comment sign (#) !
#
# LOADING DATA
# data(sw)
#  
# MASKING REGIONS WITH SPATIAL DYE BIAS
#  
# CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
# For this example, N was chosen rather small. For "real" analysis, it should be larger.
# FDR <- fdr.spatial2(sw,delta=2,N=10,av="median",edgeNA=FALSE)
#
# VISUALISATION
# sigxy.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],color.lim=c(-5,5),main="FDR")
# 
# MASKING SIGNIFICANT NEIGHBOURHOODS
# thresp <- c(0.01,0.01,0.01,0.01)
# thresn <- c(0.01,0.01,0.01,0.01)
# sw.masked <- sig.mask(sw,Sp=FDR$FDRp,Sn=FDR$FDRn,thrp=thresp,thrn=thresn)
# mxy.plot(sw.masked[,4]) # plot masked data for array 4

OLIN documentation built on Nov. 8, 2020, 7:44 p.m.