BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-2

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p>As probe affinity categories increase, the distributions shift from left to right. The black density line is the distribution from the original BGX model and illustrates the discriminatory power of the probe affinity extension

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-5

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p> on the parameter of expressed genes (left & centre). A similar improvement was observed for the IACT of the parameter, for all genes (right)

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-1

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p>ted genes between two conditions using a routine incorporated in the package

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-6

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p> (left). plots the density of the difference in the posterior distributions of a given gene between two conditions (right)

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-3

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p> Spike data set and the corresponding probes' affinity categories were estimated from the data. There is a positive correlation between estimated and true categories, particularly for high-affinity probes

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-7

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p>ted genes between two conditions using a routine incorporated in the package

BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips-4

<p><b>Copyright information:</b></p><p>Taken from "BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips"</p><p>http://www.biomedcentral.com/1471-2105/8/439</p><p>BMC Bioinformatics 2007;8():439-439.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216047.</p><p></p>l step is adapted independently for each component. The plot shows a histogram of the optimal log variance for proposals and the fixed step size used in the non-adaptive version overlaid in black, highlighting that a wide range of proposal variances are needed