Description Usage Arguments Details Value Author(s) References Examples
This function reports the results from the Frequentist and Bayesian model for hmax and for h2. It also creates an output table with the results for all the thresholds in a csv format, so the user can select additional thresholds of interest.
1  createTable(output.ratio, output.bay, dir = getwd(),h=NULL)

output.ratio 

output.bay 

dir 

h 

To select a list of interesting features from the Bayesian model we suggest two decision rules in the paper: 1) the maximum of Median(R(h)) only for the subset of credibility intervals which do not include 1; 2) the largest threshold h for which the ratio R(h) il bigger than 2.
The first one is pointing out the strongest deviation from independence, whilst the second is the largest threshold where the number of features called in common at least doubles the number of features in common under independence.
max 
The results of the R(hmax) statistic 
rule2 
The results using the rule R(h) larger than 2 (see details) 
ruleh 
The results using additional thresholds 
Alberto Cassese, Marta Blangiardo
1. M.Blangiardo and S.Richardson (2007) Statistical tools for synthesizing lists of differentially expressed features in related experiments , Genome Biology, 8, R54
1 2 3 4 5  data = simulation(n=500,GammaA=1,GammaB=1,r1=0.5,r2=0.8,
DEfirst=300,DEsecond=200,DEcommon=100)
Th< ratio(data=data$Pval)
Rh< baymod(iter=100,output.ratio=Th)
output.table < createTable(output.ratio=Th,output.bay=Rh)

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