CHANGES IN VERSION 1.29.2
----------------------------------

* Update maintainer list, adding Måns Zamore as an author

CHANGES IN VERSION 1.23.2
----------------------------------

* Fix bug where non-categorical ANOVA setting wasn't applied

CHANGES IN VERSION 1.23.1
----------------------------------

* Remove unnecessary dependency (Biobase) by calling rowMedians with matrixStats::rowMedians instead
* Fix deprecation warning by using guide = "none" instead of FALSE

CHANGES IN VERSION 1.19.7
----------------------------------

* Remove RCmdrMisc as dependency, resolving a fatal crash
  caused by updated signature of RCmdrMisc CV calculation function
* Updating code to remove deprecation warnings for ggplot2 code

CHANGES IN VERSION 1.13.2
----------------------------------

* Fixed leastRepCount setting of zero for statistics report

CHANGES IN VERSION 1.9.1
----------------------------------

* Version sync with Bioconductor

CHANGES IN VERSION 1.5.5
----------------------------------

* Updating the maintainer email

CHANGES IN VERSION 1.5.4
----------------------------------

* Option to write output as PNG files
* Option to use Limma trend=TRUE for including the intensity in its prior
* State the design groups on second page in the NormalyzerDE report

CHANGES IN VERSION 1.5.2
----------------------------------

* Updated to follow Bioconductor release cycle
* Updated to fix issues in vignette introduced by updated external packages

CHANGES IN VERSION 1.3.4
----------------------------------

* Certain datasets with fixed imputed values caused large difference in CV and MAD
  for RLR normalization, which in turn lead to a crash in the plotting functions.
  This update makes sure that the plotting can be carried out despite extreme values.

CHANGES IN VERSION 1.3.3
----------------------------------

* Extended input validation when executing NormalyzerDE using experimentObj

CHANGES IN VERSION 1.3.2
----------------------------------

* Correctly showing the number of values replaced with NA in status text

CHANGES IN VERSION 1.3.0
----------------------------------

* Sync with Bioconductor changes

CHANGES IN VERSION 1.1.16
----------------------------------

* Clearer input verification error for both incorrect fields and when values < 1 are encountered

CHANGES IN VERSION 1.1.14/15
----------------------------------

* Updating tests to avoid cyclic dependency on the NormalyzerDE package

CHANGES IN VERSION 1.1.13
----------------------------------

* Running in reduced mode for small datasets (to avoid crashing on for instance
  VSN normalization and instead omitting it)

CHANGES IN VERSION 1.1.12
----------------------------------

* Pairwise Venn-diagrams in place

CHANGES IN VERSION 1.1.11
----------------------------------

* Fix minor issue where fully empty rows were filtered before substituting
  'null' and '0' with NA

CHANGES IN VERSION 1.1.10
----------------------------------

* Add PCA visualizations showing which samples are included in each performed
    contrast

CHANGES IN VERSION 1.1.9
----------------------------------

* Extensive testing suite set up
* Bug fixes:
    - Technical replicates run through properly (previously crashed)
    - Using log-transformed input for normalization debugged
* Refactor of statistics module to separate contrast filtering from object

CHANGES IN VERSION 1.1.7
----------------------------------

* Single-replicate runs fixed so that they run through correctly

CHANGES IN VERSION 1.1.6
----------------------------------

* Add support for assigning custom thresholds for statistics report

CHANGES IN VERSION 1.1.5
----------------------------------

* Issue corrected where pattern matching for zeroToNA option incorrectly was
    matching non-zero values.

CHANGES IN VERSION 1.1.4
----------------------------------

* Allow processing of non log-transformed data

CHANGES IN VERSION 1.1.3
----------------------------------

* Additional plots for statistical comparisons, and updated look

CHANGES IN VERSION 0.99.24
----------------------------------

* Various input checks added

CHANGES IN VERSION 0.99.22
----------------------------------

* Input parsing corrected so that a clear error message is provided when the
    design matrix samples doesn't match the data matrix header

CHANGES IN VERSION 0.99.21
----------------------------------

* Documentation example fixes

CHANGES IN VERSION 0.99.20
----------------------------------

* Reactivate quantile normalization

CHANGES IN VERSION 0.99.19
----------------------------------

* Empty annotation no longer leads to crash when writing output

CHANGES IN VERSION 0.99.17/0.99.18
----------------------------------

* Very minor fix where function wasn't retrieved properly from SummarizedExperiment

CHANGES IN VERSION 0.99.16
----------------------------------

* Crash when feeding SummarizedExperiment as input is fixed
* If full rows contains only NA values they are filtered and a warning is generated

CHANGES IN VERSION 0.99.15
----------------------------------

* Corrected expected output from vapply in correlation matrix (where previous varying lengths caused crash)
* Clearer error message when providing invalid sample/group conditions to statistics module
* Issue where several identical RT-values caused crash in RT-slicing fixed
