2011-03-08: version 1.3.3

- added 'locfunc' argument to 'estimateSizeFactor' and 'estimateSizeFactorForMatrix'

2011-03-08: version 1.3.2

- added 'glmControl' argument to 'nbinomFitGLM' and 'nbinomGLMsForMatrix'

2011-02-11: version 1.3.2

- updated CITATION

2010-09-06: version 1.1.13

- corrected the sometimes missing names attribute in rawVarFuncTable

2010-09-06: version 1.1.12

- fixed a bug in the 'resVarB' column of the result of 'nbinomTest'.

2010-08-17: version 1.1.11

- 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.

2010-08-17: version 1.1.10

- fixed bug in makeExampleCountDataSet: colnames were wrong

2010-07-21: version 1.1.9

- removed the variance adjustment factors introduced earlier; they caused
  more trouble than they were worth.

2010-07-09: version 1.1.8

- GLM functionality added but not yet documented

2010-06-05: version 1.1.7

- no change, just bumped version number as the build server seemed to have
  gotten confused

2010-06-02: version 1.1.6

- changed arguments for estimateVarianceFunctionsin preparation for a planned new
  feature; instead of pool=FALSE or pool=TRUE, use method="normal" or 
  method="blind".

2010-06-01: version 1.1.5

- fixed a small bug that caused p values to sometimes slighly exceed 1.0
  due to rounding errors

2010-05-15: version 1.1.4

- 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

2010-05-06: version 1.1.3

- added a CITATION file

2010-05-03: version 1.1.2

- 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.    

2010-04-29: version 1.1.1

- 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
  
