Dear developers, The package HTSFilter is now available in the Bioc devel branch. HTSFilter implements a novel independent filtering procedure using a data-based threshold for observations with low, constant levels of expression in replicated RNA sequencing data. In particular, it features the following: - Data-driven way to select an appropriate filtering threshold, rather than an arbitrarily chosen threshold (e.g., mean counts < 5) - Filtering of observations that appear to generate an uninformative signal and have little chance of being identified as differentially expressed, thus reducing the number of tests to be performed - Seamless integration into the DESeq (S4 class CountDataSet) and edgeR (D3 classes DGEList, DGEExact, DGEGLM, DGELRT) pipelines for differential analysis Thanks, and I look forward to hearing your feedback. Andrea
_____________________________________________ Dr. Andrea Rau Institut National de la Recherche Agronomique (GABI / PSGen) Domaine de Vilvert, B?timent 211 78352 Jouy-en-Josas CEDEX Tel: (+33) (0) 1.34.65.22.82 Fax: (+33) (0) 1.34.65.22.10 http://www.jouy.inra.fr/gabi