version 1.9.12: (2012-09-05) - added function newCountDataSetFromHTSeqCount version 1.9.7: (2012-05-25) - fixed handling of rank-deficient observations now also in estimateDispersions version 1.9.6: - fixed that varianceStabilizingTransformation was missing in exports version 1.9.5: - added function plotDispEsts version 1.9.4: (2012-04-24) - fixed handling of rank-deficient observations version 1.9.2: (2012-04-05) - fixed bug in pooled-CR dispersion estimation version 1.9.1: (2012-04-01) - Added a new function 'varianceStabilizingTransformation' version 1.7.10: (2011-03-26) - Added pooled-CR method. - Fixed error message for insufficient replication. version 1.7.9: (2011-03-16) - Fixed error in vignette. - Silenced warnings from nbinomFitGLM about convergence; this information is given in the result anyway. version 1.7.8: (2011-03-15) - The VST is now roughly equal to log2 for local dispersion fits, too. version 1.7.7: (2011-03-15) - changed the variance stabilizing transformation once more; this time it is hopefully correct. The derivation of the formula is now documented in the new file vst.pdf. version 1.7.6: - fixed regression bug in getVarianceStabilizedData: the formula for parametric dispersion fit was wrong since I "fixed" the factor to get log2 asymptotic behaviour. version 1.7.1 - 1.7.5: - various changes to vignette by whuber version 1.6.0 / 1.7.0: (Summary of important changes between Bioc release 2.8 to 2.9) - changes to dispersion estimation scheme to improve handling of outliers (see vignette for details) - refactorized the workflow and overhauled and expanded the vignette (see there for changes to user interface) - various changes and bug fixes (see appendix in vignette and NEWS file) version 1.5.29: (2011-10-10) - fixed a bug in parametricDispersionFit. (Thanks to Alejandro Reyes for spotting and fixing this one.) version 1.5.27: (2011-10-18) - method="pooled" is now default in estimateDispersions - added 'fitInfo' accessor function version 1.5.24: (2011-08-10) - fitNbinomGLM no longer stops when glm.fit throws an error version 1.5.23: (2011-07-14) - fixed bug in 'nbinomTest' again; now using a symmetric two-tailed test (i.e., the one-tailed p value is doubled) - added warning in case of method='blind' if not used together with sharingMode='fit-only' version 1.5.22: (2011-07-14) - fixed bug in 'nbinomTest' that led to wrong p values for dispersions larger than 1 version 1.5.21: (2011-07-14) - minor changes to vignette version 1.5.20: (2011-07-07) - fixed bug in 'getVarianceStabilizedData' - more informative error message if parametric fit fails versions 1.5.1 to 1.5.19: (2011-06 / 2011-07) refactorized the way how dispersion estimation is handled, overhauled the vignette - vignette now uses data from 'pasilla' package as example - GLMs explained in vignette - 'estimateVarianceFunctions' renamed to 'estimateDispersions' - estimateDispersions now stores intermediate results in 'fitInfo' slot - new functionality for 'estimateDispersion': 'sharingMode' option with new sharing modes 'maximum' and 'gene-est-only'; 'fitType' with new fitting type 'parametric'; changed defaults for these; new method 'pooled-CR' to do edgeR-style CR estimation etc. - several diagnostic functions removed - lots of further small changes version 1.3.3: (2011-03-08) - added 'locfunc' argument to 'estimateSizeFactor' and 'estimateSizeFactorForMatrix' version 1.3.2: (2011-03-08) - added 'glmControl' argument to 'nbinomFitGLM' and 'nbinomGLMsForMatrix' version 1.3.2: (2011-02-11) - updated CITATION version 1.1.13: (2010-09-06) - corrected the sometimes missing names attribute in rawVarFuncTable version 1.1.12: (2010-09-06) - fixed a bug in the 'resVarB' column of the result of 'nbinomTest'. version 1.1.11: (2010-08-17) - fixed a bug in getVarianceStabilizedData; it failed to preserve normalization. This is because the transformation function for each sample were different if the size factors differed. The function now uses an average size factor. However, the veriance stabilizing transformation is still not perfect: the variance still increases slightly with the mean. This needs a bit more work As an alternative to judge similarity of samples, I have added two new functions, getRawScvForSamplePair and getRawScvDistanceMatrix. See their help pages. version 1.1.10: (2010-08-17) - fixed bug in makeExampleCountDataSet: colnames were wrong version 1.1.9: (2010-07-21) - removed the variance adjustment factors introduced earlier; they caused more trouble than they were worth. version 1.1.8: (2010-07-09) - GLM functionality added but not yet documented version 1.1.7: (2010-06-05) - no change, just bumped version number as the build server seemed to have gotten confused version 1.1.6: (2010-06-02) - changed arguments for estimateVarianceFunctionsin preparation for a planned new feature; instead of pool=FALSE or pool=TRUE, use method="normal" or method="blind". version 1.1.5: (2010-06-01) - fixed a small bug that caused p values to sometimes slighly exceed 1.0 due to rounding errors version 1.1.4: (2010-05-15) - corrected a serious documentation bug: the effect of the variance adjustment factors was described the wrong way round - changed scvPlot: now does a bias correction by default version 1.1.3: (2010-05-06) - added a CITATION file version 1.1.2: (2010-05-03) - replaced the C function to calculate the p values. The new version is now a bit more conservative with its approximation, trying to ensure that p values are always rather approximated as too high. Furthermore, it considers the values 0 and kS as critical points, too, which makes a difference at very high overdispersion. - changed the default value for the accuracy guidance 'eps' from 3e-3 to 1e-4, as the former seemed to have been a bit too high. (The approximation broke down in rare cases.) - The 'eps' parameter is now exposed in 'nbinomTest' as well. version 1.1.1: (2010-04-29) - added "variance adjustment factors" in order to allow for manual scaling of the raw variance estimate in case that the residual ECDF plots indicate a bad fit - fixed a bug which caused the resVarB column of the data frame returned by nbinomTest to be wrong - changed the scvPlot function to now show conditions rather than raw variance functions - changed the way how 'rawVarFunc' interprets its second argument - updated the vignette