computeObservedFstat {biclust}  R Documentation 
Diagnostic F Statistic Calculation
Description
Functions for obtaining F statistics within bicluster and the significance levels. The main effects considered are row, column and interaction effect.
Usage
computeObservedFstat(x, bicResult, number)
Arguments
x 
Data Matrix 
bicResult 

number 
Number of bicluster in the output for computing observed statistics 
Details
Fstatistics are calculated from the twoway ANOVA mode with row anc column effect. The full model with interaction is unidentifiable, thus, Tukey's test for nonadditivity is used to detect an interaction within a bicluster. pvalues are obtained from assymptotic F distributions.
Value
Data frame with three rows ("Row Effect", "Column Effect", "Tukey test") and 2 columns for corresponding statistics (Fstat) and their pvalues (PValue). 2
Author(s)
Tatsiana KHAMIAKOVA tatsiana.khamiakova@uhasselt.be
See Also
diagnosticTest
, diagnosticPlot2
, ChiaKaruturi
, diagnoseColRow
Examples
#simulate dataset with 1 bicluster #
xmat<matrix(rnorm(50*50,0,0.25),50,50) # background noise only
rowSize < 20 #number of rows in a bicluster
colSize < 10 #number of columns in a bicluster
a1<rnorm(rowSize,1,0.1) #sample row effect from N(0,0.1) #adding a coherent values bicluster:
b1<rnorm((colSize),2,0.25) #sample column effect from N(0,0.05)
mu<0.01 #constant value signal
for ( i in 1 : rowSize){
for(j in 1: (colSize)){
xmat[i,j] < xmat[i,j] + mu + a1[i] + b1[j]
}
}
#obtain a bicluster by running an algorithm#
plaidmab < biclust(x=xmat, method=BCPlaid(), cluster="b", fit.model = y ~ m + a+ b,
background = TRUE, row.release = 0.6, col.release = 0.7, shuffle = 50, back.fit = 5,
max.layers = 1, iter.startup = 100, iter.layer = 100, verbose = TRUE)
#Calculate statistics and their pvalues to infer about the structure within bicluster:
Structure < computeObservedFstat(x=xmat, bicResult = plaidmab, number = 1)