fdr.int2 {OLIN} | R Documentation |
This function assesses the significance of intensity-dependent bias by an one-sided random permutation test. The observed average values of logged fold-changes within an intensity neighbourhood are compared to an empirical distribution generated by random permutation. The significance is given by the false discovery rate.
fdr.int2(object,delta=50,N=100,av="median")
object |
object of class marrayRaw or marrayNorm |
delta |
integer determining the size of the neighbourhood. The actual window size is
(2 * delta+1 ). |
N |
number of random permutations performed for generation of empirical distribution |
av |
averaging of M within neighbourhood by mean or median (default) |
This function fdr.int2
is basically the same as fdr.int
except for
differences in their in- and output format. For the details about the functionality, see fdr.int
.
This function will be merged with fdr.int
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