sigint.plot {OLIN} | R Documentation |
This function visualises the significance of intensity-dependent bias.
sigint.plot(A,M,Sp,Sn,ylim=c(-3,-3),...)
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 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 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 |
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 M
of
spot intensity neighbourhoods are presented by red colour; the significance for negative
median/mean of M
of
spot intensity neighbourhoods are presented by green colour. The ordinate axis (y-axis) give the
log10-transformed FDR or p-values.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
# 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))