calcSRmatMod

A matrix containing fold changes or ratios from a biological
 dataset to process for searching differentially expressed
 genes or for detecting recurrent copy number aberrations 
 regions: <code>fcMat</code>.

xdata

A vector of sample label names which should appear in the columns
 of the matrix fcMat: <code>samp</code>.

samp

A scalar equals to 0 or 1. The value 0 (default) means that
 values in the matrix "fcMat" are expressed in a log2 scale:
 <code>log2.opt</code> = 0

log2.opt

A scalar between 0 and 0.5. The value 0.25 (default) means
 that 25% of the lower and the upper rank values for each gene 
 are not used for computing the statistic "ri", i.e. the 
 interquartile range rank values are averaged:
 <code>trim.opt</code> = 0.25

trim.opt

This is an internal function used to calculate the sorted
rank matrix. It is used in the functions: fcrosMod() and pfcoMod().

A fold change rank based method is presented to search for genes with changing
expression and to detect recurrent chromosomal copy number aberrations. This
method may be useful for high-throughput biological data (micro-array, sequencing, ...).
Probabilities are associated with genes or probes in the data set and there is no
problem of multiple tests when using this method. For array-based comparative genomic
hybridization data, segmentation results are obtained by merging the significant
probes detected.

calcSRmatMod: Calculation of the sorted rank matrix from the dataset

Description

Usage

Arguments

References

Examples