threshold {MixThres}R Documentation

Threshold Hybridization

Description

Define a threshold hybridization in DNA microarray experiments.

Usage

threshold(MixThres, crit = 1e-04, fileGRAPH = NULL, fileOUT = NULL, sep = "\t", ...)

Arguments

MixThres an object of class MixThres.
crit precision used to define the hybridization threshold
fileGRAPH the name of the file where graphic is created. If fileGRAPH=NULL no graphic is made.
fileOUT the name of the file where output are created. If fileOUT=NULL no output file is created.
sep the field separator string used for writing the output file. Values within each row of x are separated by this string.
... others arguments to write.table

Details

The threshold above which a probe is declared as being hybridized is defined as following :
T(crit) = max(y_g |{k^*_g}<widehat{K} exists s ε (1,...,k^*_{g-1}), widehat{tau}_{sg} >=q crit)
In other words, intensity values are ranked by descending order, for each probe g $k^*_g$ is determined using the Maximum A Posteriori rule. Then if $k^*_g$ differs from the component with the highest mean $widehat{K}$, the posterior probability of belonging to each component with lower mean than $μ_{k^*_g}$ is calculated. The threshold is then defined as the first intensity value such that one of the calculated posterior probabilities is greater than crit.

Value

an object of class MixThres. Three components are added :

threshold the hybridization threshold.
crit the precision value associated to the hybridization threshold.
Hybrid the hybridization index precising wether the spot is hybridized (1) or not (0).

Author(s)

J. Aubert

References

Picard et al., Using mixture models to define a hybridization threshold in DNA microarray experiments.

See Also

hybridization


[Package MixThres version 1.0 Index]