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