http://precedings.nature.com/tags/contingency%20table Recently posted documents tagged with 'contingency table' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/369/version/1 As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table forthe enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation. http://precedings.nature.com/documents/369/version/1 Fri, 06 Jul 2007 04:42:39 UTC ProbCD: enrichment analysis accounting for categorization uncertainty hdl:10101/npre.2007.369.1 2007-07-06 Ricardo Vêncio Nature Precedings 2007-07-06T04:42:39Z Manuscript Biotechnology Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/2.5/