RELEASE HISTORY OF THE "PAA" PACKAGE
===========================================

CHANGES IN PAA VERSION 1.3.3 [2015-07-14]:
-----------------------------------------------
GENERAL
* No changes.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* Bug in the function loadGPR() fixed (due to a wrong regular expression some data rows
  were not imported from gpe files in PAA versions 1.3.2 and 1.3.1 -> the bug was not
  relevant for the versions 1.3.0 and older).

CHANGES IN PAA VERSION 1.3.2 [2015-06-22]:
-----------------------------------------------
GENERAL
* Update to the latest R version which has been released a few days ago (2015-06-18).
* Built with R-3.2.1 

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* NEWS file of version 1.3.1 corrected (wrong version number for the last update in the
  NEWS file).

BUG FIXES
* No changes.

CHANGES IN PAA VERSION 1.3.1 [2015-06-17]:
-----------------------------------------------
GENERAL
* The optional rlm normalization (for ProtoArrays) used by the functions normalizeArrays(),
  plotNormMethods() and plotMAPlots() has been completely reimplemented in order to fix
  some bugs and simplify the usage of these functions (details: see below).
* Built with R-3.2.0 

NEW FEATURES
* No changes.

IMPROVEMENTS
* Due to the modification of the EListRaw objects for ProtoArrays the usage of the
  functions normalizeArrays(), plotNormMethods() and plotMAPlots() is simplified since
  some obsolete arguments have been removed (see 'MODIFICATIONS'). Esp., the provision of
  a second controls-specific EListRaw object for controls data and information was too
  complex and has confused some users. Now all control spot-specific data and information
  are stored together with probe-specific data and information in one extended EListRaw
  object.

MODIFICATIONS
* On the one hand, the arguments 'controls.elist', 'gpr.path', 'targets.path' and
  'contr.names' have been removed from the functions normalizeArrays(), plotNormMethods()
  and plotMAPlots(). On the other hand, the argument 'controls' has been added to the
  functions normalizeArrays(), plotNormMethods() and plotMAPlots().

BUG FIXES
* Due to the re-implementation of the optional rlm normalization (for ProtoArrays)
  used by the functions normalizeArrays(), plotNormMethods(), plotMAPlots(), all bugs
  that have been reported by users since version 1.0.0 are fixed.

CHANGES IN PAA VERSION 1.1.1 [2015-03-13]:
-----------------------------------------------
GENERAL
* No changes.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* Bug in the function batchAdjust() removed.
  Because the argument "mod" was not passed as factor to sva's
  function ComBat() errors were thrown and execution stopped
  for the latest versions of sva. This has been corrected.

CHANGES IN PAA VERSION 1.0.0 [2014-10-13]:
-----------------------------------------------
GENERAL
* First release version.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* No changes.

CHANGES IN PAA VERSION 0.99.4 [2014-10-03]:
-----------------------------------------------
GENERAL
* First release version.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* Corrected \VignetteIndexEntry{} in the vignette Rnw file.

CHANGES IN PAA VERSION 0.99.3 [2014-10-02]:
-----------------------------------------------
GENERAL
* License changed from GPL-3 to “BSD_3_clause + file LICENSE” due to license compatibility.

NEW FEATURES
* No changes.

IMPROVEMENTS
* Some dummy gpr files added to demonstrate loadGPR() in man pages and vignette.
* First unit tests added.
* Native routines registered.
* Checking runtimes improved.

MODIFICATIONS
* No changes.

BUG FIXES
* Bug fixes in the vignette (e.g., \comment to \bioccomment). Missing vignette preambel added.
* Bug fixes in the code (e.g., max. line length of 80 characters ensured, "FALSE" instead of "F").
* Internal functions removed from export in the NAMESPACE.

CHANGES IN PAA VERSION 0.99.2 [2014-08-05]:
-----------------------------------------------
GENERAL
* No changes.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* Minor change in the vignette (changing the selectFeatures()-option selection.method="rj.rfe"
to selection.method="rf.rfe" to make the code chunks runable on systems without Random Jungle installed).

CHANGES IN PAA VERSION 0.99.1 [2014-08-05]:
-----------------------------------------------
GENERAL
* No changes.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* Hard coded temp directory replaced by a tempdir()-based solution.

CHANGES IN PAA VERSION 0.99.0 [2014-08-03]:
-----------------------------------------------
GENERAL
* NEWS file added.
* Vignette completed.
* Documentation completed.
* General compatibility for Windows, Mac OS X and Linux ensured.

NEW FEATURES
* No changes.

IMPROVEMENTS
* No changes.

MODIFICATIONS
* No changes.

BUG FIXES
* No changes.