extractFeatures.T: Extracting the lists of features of interest
In sdef: Synthesizing List of Differentially Expressed Features

Description Usage Arguments Details Value Author(s) References Examples

The function returns the list of features in common using the hmax rule (Frequentist model).

1	extractFeatures.T(output.ratio, feat.names)

`output.ratio`	`The output object from the Frequentist model (ratio function)`
`feat.names`	`names of the features (e.g Affy ID for genes)`

To select a list of interesting features from the frequentist model we suggest a decision rules in the paper: the maximum of T(h)=nb genes in common/nb genes in common under the hypothesis of independence. It is pointing out the strongest deviation from independence.

The function returns an object of the class list. Each element is a matrix where the first column contains the name of the features while the other columns contain the p-values* from the experiments. It also saves a .csv file with the same information.

*instead of the p-values any other measure used to rank the features in the experiments can be used.

max

The list of features in common selected on the basis of the threshold associated to T(hmax)

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

data = simulation(n=500,GammaA=1,GammaB=1,r1=0.5,r2=0.8,
DEfirst=300,DEsecond=200,DEcommon=100)
Th<- ratio(data=data$Pval)
feat.names = data$names
feat.lists.T <- extractFeatures.T(output.ratio=Th,
feat.names=feat.names)