crosshyb_func {crosshybDetector}R Documentation

Computing cross-hybrization pvalues

Description

It is usually called from within crosshyb, but can be invoked directly. The algorithm is described into the paper in References section

Usage

crosshyb_func(input, seqList, mysub, numPermut,
              probes, satValue, maxProbes, delta = 10)

Arguments

input A dataframe containing the i) raw intensity value, ii) the probe type (e.g. spike, probes, negative,...) and iii) the probe name
seqList An object of class AASequenceList created with readFasta
mysub Substitution matrix to be used for the alignment
numPermut Number of permutations for Monte Carlo simulations
probes A vector with the probes to be analyzed (e.g. probes, spike, etc)
satValue The value corresponding to saturated probes
maxProbes The maximun number of probes to analyze
delta Threshold for difference in melting temperature. Pairs of probes whose delta Tm is lower than delta are considered as similar. Delta Tm i,k is computed as Tm i,i - Tm i,k, where Tm i,i is the Tm of the percect pairing probe i vs probe i and Tm i,k is the Tm of the imperfect pairing probe i vs probe k

Value

A list containing:

data Dataframe with three columns containing the results of the analysis for the putative corruptor probes. Contains: i) the probe number, ii) the probe name and iii) the pvalue based on Monte Carlo simulations of being a corruptor (pvalue is corrected for multiple testing)
children A list containing the corrupted probes for each putative corruptor

Author(s)

Paolo Uva

References

Uva, P., and de Rinaldis, E. CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments. BMC Bioinformatics 2008, 9:485

See Also

crosshyb


[Package crosshybDetector version 1.0.4 Index]