sigint.plot: Visualisation of significance of intensity-dependent bias In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

Description

This function visualises the significance of intensity-dependent bias.

Usage

 `1` ```sigint.plot(A,M,Sp,Sn,ylim=c(-3,-3),...) ```

Arguments

 `A` vector of average logged spot intensity `M` vector of logged fold changes `Sp` vector of false discovery rate or p-values for positive deviation of median/mean of \code{M} as produced by `fdr.int` or `p.int` `Sn` vector of false discovery rate or p-values for negative deviation of median/mean of \code{M} as produced by `fdr.int` or `p.int` `ylim` vector of minimal log10(fdr) or log10(p-value) to be visualised corresponding to `Sp` and `Sn`. FDR or p-values smaller than these values will be set equal to these threshold values for visualisation. `...` Further optional graphical parameter for the `plot` function generating the MA plot

Details

The function `sigint.plot` produces a MA-plot of the significance (`Sp`,`Sn`) generated by `fdr.int` or `p.int`. The abscissa (x-axis) is shows by the average logged spot intensity `A=0.5*(log(Cy3)+log(Cy5))`; the ordinate axis (y-axis) shows the log10(FDR) or log10(p) given by `FDRp` or `Pn` and `FDRn` or `Pn`. The significance for positive median/mean of \code{M} of spot intensity neighbourhoods are presented by red colour; the significance for negative median/mean of \code{M} of spot intensity neighbourhoods are presented by green colour. The ordinate axis (y-axis) give the log10-transformed FDR or p-values.

Author(s)

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

See Also

`sigxy.plot`, `fdr.int`, `p.int`

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15``` ```# To run these examples, "un-comment" them! # # LOADING DATA NOT-NORMALISED # data(sw) # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # This can take a while! For testing, you may choose a smaller N. # FDR <- fdr.int(maA(sw)[,1],maM(sw)[,1],delta=50,N=100,av="median") # VISUALISATION OF RESULTS # sigint.plot(maA(sw)[,1],maM(sw)[,1],FDR\$FDRp,FDR\$FDRn,c(-5,-5)) # data(sw.olin) # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # F <- fdr.int(maA(sw.olin)[,1],maM(sw.olin)[,1],delta=50,N=100,av="median") # VISUALISATION OF RESULTS # sigint.plot(maA(sw.olin)[,1],maM(sw.olin)[,1],FDR\$FDRp,FDR\$FDRn,c(-5,-5)) ```

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