threshold {MixThres} | R Documentation |
Define a threshold hybridization in DNA microarray experiments.
threshold(MixThres, crit = 1e-04, fileGRAPH = NULL, fileOUT = NULL, sep = "\t", ...)
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 |
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.
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). |
J. Aubert
Picard et al., Using mixture models to define a hybridization threshold in DNA microarray experiments.