Package: BitSeq =============== Version 1.2.2 (29.1.2013) - bug fix for getExpression which caused occasional crash when using non-uniform model Version 1.2.1 (6.11.2012) - bug fixes for parsing gapped alignments and half-alignments of paired end reads Version: 1.2.0 (27.9.2012) - IMPORTANT change: the way samples-files are passed to getDE, estimateHyperPar, estimateDE changed. -> instead of providing 2 vectors of filenames for each condition, the files are passed as a list of vectors, each vector containing filenames for one condition (allowing use of more than 2 conditions) - new internal structure (not visible to user) - estimateExpression has a new convergence criterion which should result in producing fewer samples (faster and dropping the use of MCMC_scaleReduction and MCMC_samplesNmax flags) -> estimateExpressionLegacy uses the original convergence criterion - library normalization option for getDE, estimateDE, estimateHyperPar, getMeanVariance (in form of providing the normalization constants, for getting the constants please use edgeR or similar) Version: 1.0.1 (30.4.2012) Version: 1.1.1 (30.4.2012) - fixed bug in estimateExpression (reading file with probabilities occasionally failed when transcript information file was not specified) - improved manual, replaced overflowing lines - added option "pretend" to produce C++ calls Version: 1.0.0 - First Bioconductor release of BitSeq