MixThres


MixThres est un package permettant la définition d’un seuil d’hybridation à partir de modèles de mélange sur la distribution d’un signal

Even if one of the major applications of two-color DNA microarray hybridizations is to detect differentially expressed genes using intensity log-ratios, single channel signals provide also useful information as absolute value measurements which allow the description of gene expression patterns. In this context, it becomes crucial to determine the set of probes that hybridize, that is for which the intensity signal is greater than a hybridization threshold to be fixed. Existing procedures are either an arbitrary thresholding or require the knowledge of a population of non-hybridized probes. In this work we present the MixThres method to determine an adaptive hybridization threshold from intensity levels of the complete set of probes hybridized on a chip. We define a hybridization threshold based on the histogram of the probe intensity values. Our procedure is divided into two steps. First the intensity distribution is estimated using mixture models. Second a hybridization threshold is defined from the components of the mixture. We validate our method on DNA tiling array and expression array data. We show that our method has a good reproducibility, its specificity is greater than 97 % and its precision of 88 %. The R package MixThres is available at http://www.agroparistech.fr/mia/outil.htm


Informations générales
Informations spécifiques
Langage(s) de développement
R
N° de version courante
V1.0
Date de la version courante
OS supporté
Type de licence


Porteur(s)
Unité
MIA-Paris
Département co-porteur
BAP
Auteur(s)
Julie Aubert
Marie-Laure Martin-Magniette
Contact
julie.aubert@agroparistech.fr
Publication de référence


 

 

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