gprege Quick Guide

Abstract

The gprege package implements our methodology of Gaussian process regression models for the analysis of microarray time series. The package can be used to filter quiet genes and quantify/rank differential expression in time-series expression ratios. The purpose of this quick guide is to present a few examples of using gprege. 2 Citing gprege Citing gprege in publications will involve citing the methodology paper [Kalaitzis and Lawrence, 2011] that the software is based on as well as citing the software package itself. 3 Introductory example analysis- TP63 microarray data In this section we introduce the main functions of the gprege package by repeating some of the analysis from the BMC Bioinformatics paper [Kalaitzis and Lawrence, 2011]. 3.1 Installing the gprege package The recommended way to install gprege is to use the biocLite function available from the bioconductor website. Installing in this way should ensure that all appropriate dependencies are met