CHANGES IN VERSION 1.2.4
------------------------

    o Reduced the amount of filtering from Cook's cutoff:
      maximum no longer includes samples from experimental groups 
      with only 2 samples, the default F quantile is raised to 0.99,
      and a robust estimate of dispersion is used to calculate
      Cook's distance instead of the fitted dispersion.

CHANGES IN VERSION 1.1.32
-------------------------

    o By default, use QR decomposition on the design matrix X.
      This stabilizes the GLM fitting. Can be turned off with
      the useQR argument of nbinomWaldTest() and nbinomLRT().

    o Allow for "frozen" normalization of new samples using
      previous estimated parameters for the functions: 
      estimateSizeFactors(), varianceStabilizingTransformation(),
      and rlogTransformation(). See manual pages for details and
      examples.

CHANGES IN VERSION 1.1.31
-------------------------

    o The adjustment of p-values and use of Cook's distance
      for outlier detection is moved to results() function
      instead of nbinomWaldTest(), nbinomLRT(), or DESeq().
      This allows the user to change parameter settings 
      without having to refit the model.

CHANGES IN VERSION 1.1.24
-------------------------

    o The results() function allows the user to specify a 
      contrast of coefficients, either using the names of 
      the factor and levels, or using a numeric contrast 
      vector. Contrasts are only available for the Wald test
      differential analysis.

CHANGES IN VERSION 1.1.23
-------------------------

    o The results() function automatically performs independent
      filtering using the genefilter package and optimizing 
      over the mean of normalized counts.

CHANGES IN VERSION 1.1.21
-------------------------

    o The regularized log transformation uses the fitted
      dispersions instead of the MAP dispersions. This prevents
      large, true log fold changes from being moderated due to
      a large dispersion estimate blind to the design formula.
      This behavior is also more consistent with the variance
      stabilizing transformation.

CHANGES IN VERSION 1.0.10
-------------------------

    o Outlier detection: Cook's distances are calculated for each
      sample per gene and the matrix is stored in the assays list.
      These values are used to determine genes in which a single 
      sample disproportionately influences the fitted coefficients. 
      These genes are flagged and the p-values set to NA.
      The argument 'cooksCutoff' of nbinomWaldTest() and 
      nbinomLRT() can be used to control this functionality.


CHANGES IN VERSION 1.0.0
------------------------

    o Base class: SummarizedExperiment is used as the superclass 
      for storing the data.

    o Workflow: The wrapper function DESeq() performs all steps 
      for a differential expression analysis. Individual steps are 
      still accessible.

    o Statistics: Incorporation of prior distributions into the 
      estimation of dispersions and fold changes (empirical-Bayes 
      shrinkage). A Wald test for significance is provided as the 
      default inference method, with the likelihood ratio test of 
      the previous version also available.

    o Normalization: it is possible to provide a matrix of sample- 
      *and* gene-specific normalization factors