| sigint.plot2 {OLIN} | R Documentation |
This function produce visualises the significance of intensity-dependent bias.
sigint.plot2(object,Sp,Sn,ylim=c(-3,-3),...)
object |
object of class marrayRaw or marrayNorm |
Sp |
vector of false discovery rate or p-values for positive deviation of median/mean of M
as produced by fdr.int2 or p.int2 |
Sn |
vector of false discovery rate or p-values for negative deviation of median/mean of M
as produced by fdr.int2 or p.int2 |
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 |
The function sigint.plot2 only differs from sigint.plot in its input arguments.
The functionality is the same. For details, see sigint.plot.
This function will be merged with sigint.plot in future versions.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
# To run these examples, delete the comment signs (#) in front of the commands. # # LOADING DATA NOT-NORMALISED # data(sw) # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS # For this example, N was chosen rather small. For "real" analysis, it should be larger. # FDR <- fdr.int2(sw,delta=50,N=10,av="median") # VISUALISATION OF RESULTS # sigint.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],c(-5,-5)) # array 1 # sigint.plot2(sw[,4],FDR$FDRp[[4]],FDR$FDRn[[4]],c(-5,-5)) # array 4