This manual shows how to use the mombf library to compute Moment and inverse Moment Bayes factors (Mom BF and iMom BF, respectively). The intuitive appeal of Mom and iMom BF is that they represent prior beliefs under the alternative hypothesis which are fundamentally different from those under the null hypothesis. Mathematically, when the null hypothesis is true they present better convergence ...

Moreover, model selection and evaluation of prediction rules proves to be highly difficult in this situation for several reasons. Firstly, the hazard of overfitting, which is common to all prediction problems, is increased by high dimensionality. Secondly, the usual evaluation scheme based on the splitting into learning and test data sets often applies only partially in the case of small sample...

The RankProd package contains functions for the analysis of gene expression microarray data, in particular the identification of differentially expressed genes. RankProd utilizes the so called rank product non-parametric method (Breitling et al., 2004, FEBS Letters 573:83) to identify up-regulated or down-regulated genes under one condition against another condition, e.g. two different treatmen...

3 Differential expression analysis 4 3.1 Defining data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3.2 Clustering of probes evaluation of probe expression profiles . . . . . . . . . . . . 5 3.3 Differential expression analysis from probes to annotation . . . . . . . . . . . . . 6 3.4 Functional annotation analysis . . . . . . . . . . . . . . . . . . . . . . ....

This is the vignette of the Bioconductor add-on package GeneSelector which contains methods to assess quantitatively the variability among multiple gene rankings, obtained by using altered datasets or several ranking procedures. The resulting multiplicity problem is addressed by functionality for rank aggregation.

Many transcription factors (TFs) regulate gene expression by binding to specific DNA motifs near genes. Often the regulation of gene expression is not only controlled by one TF, but by many TFs together, that can either interact in a cooperative manner or interfere with each other. In recent years high thoughput methods, like ChIP-Seq, have become available to produce large amounts of data, tha...

The MultiMed package implements a permutation method which adjusts for “multiple comparisons” when testing whether multiple biomarkers are mediators between a known risk factor and a disease. The approach is described in the companion paper [Boca et al., 2014], “Testing multiple biological mediators simultaneously.” This method can significantly improve the power to detect mediators over the st...

Many transcription factors (TFs) regulate gene expression by binding to specific DNA motifs near genes. Often the regulation of gene expression is not only controlled by one TF, but by many TFs together, that can either interact in a cooperative manner or interfere with each other. In recent years high thoughput methods, like ChIP-Seq, have become available to produce large amounts of data, tha...

3 Network analysis 15 3.1 Simulation of state transitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.2 Identification of attractors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 3.3 Markov chain simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 3.4 Robustness assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . ...

OBJECTIVE To assess variations in adherence to guidelines for management of postpartum hemorrhage (PPH) among midwives. METHODS A multicentre vignette-based study was e-mailed to a random sample of midwives from 145 maternity units in France. They were asked to describe how they would manage the PPH described in 2 case-vignettes. These previously validated case-vignettes described 2 different...