sig.mask {OLIN} | R Documentation

## Masking of data based on significance testing

### 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

[Package OLIN version 1.70.0 Index]