Version: 1.7.1
Date: 2016-05-13
Category: GENERAL
Text: Built with the latest R version (R-3.2.4 Revised).

Version: 1.7.1
Date: 2016-05-13
Category: GENERAL
Text: Built with the latest Rtools version (Rtools 3.3).

Version: 1.7.1
Date: 2016-05-13
Category: GENERAL
Text: Update of the PAA citation: PAA applications note, Turewicz et
        al., Bioinformatics, 2016, PMID: 26803161, added to the
        CITATION file.

Version: 1.7.1
Date: 2016-05-13
Category: GENERAL
Text: Update of the URL in the DESCTIPTION file.

Version: 1.7.1
Date: 2016-05-13
Category: GENERAL
Text: Correction of some typos in the documentation.

Version: 1.7.1
Date: 2016-05-13
Category: GENERAL
Text: Update of the vignette to demonstrate the new features.

Version: 1.7.1
Date: 2016-05-13
Category: NEW FEATURES
Text: New function: batchFilter.anova() for multi-batch scenarios.

Version: 1.7.1
Date: 2016-05-13
Category: NEW FEATURES
Text: New function: plotFeaturesHeatmap.2() as an alternative to
        plotFeaturesHeatmap().

Version: 1.7.1
Date: 2016-05-13
Category: NEW FEATURES
Text: New arguments for loadGPR(): "description",
        "description.features" and "description.discard" for data
        import when gpr files don't provide the column "Description".
        Furthermore, new dummy data has been added to the package in
        order to demonstrate this new feature.

Version: 1.7.1
Date: 2016-05-13
Category: NEW FEATURES
Text: Now the customized object classes EListRaw and EList contain the
        new component "array.type" added by loadGPR when the data is
        imported.

Version: 1.7.1
Date: 2016-05-13
Category: IMPROVEMENTS
Text: Additional and more informative error messages added.

Version: 1.7.1
Date: 2016-05-13
Category: IMPROVEMENTS
Text: The function plotArray() is more flexible. Now, not only
        ProtoArrays can be plotted. Moreover, now the plot can be saved
        also as png file.

Version: 1.7.1
Date: 2016-05-13
Category: MODIFICATIONS
Text: The loadGPR() and plotArray()-argument "protoarray.aggregation"
        has been renamed to "aggregation" and the default value has
        been changed to "none".

Version: 1.7.1
Date: 2016-05-13
Category: MODIFICATIONS
Text: The loadGPR() argument "array.type" is mandatory now.

Version: 1.7.1
Date: 2016-05-13
Category: BUG FIXES
Text: Plots created during rlm normalization by normalizeArrays() were
        in logE scale and not in log2 scale. This has been fixed.

Version: 1.7.1
Date: 2016-05-13
Category: BUG FIXES
Text: Correction of regular expressions for rlm normalization in
        normalizeArrays() and for data import in loadGPR().

Version: 1.5.1
Date: 2015-10-20
Category: GENERAL
Text: No changes.

Version: 1.5.1
Date: 2015-10-20
Category: NEW FEATURES
Text: The new function plotArray() is available. It can be used for
        visual inspection of ProtoArrays as well as for the monitoring
        of the impact of any pre-processing method applied to the data.
        In order to support the plotting of ProtoArrays before
        duplicate aggregation and to mimic the original scan image of
        ProtoArrays, now loadGPR() supports the option
        protoarray.aggregation="none". Finally, the vignette has been
        updated in order to describe the new function via an exemplary
        ProtoArray showing a spatial bias.

Version: 1.5.1
Date: 2015-10-20
Category: IMPROVEMENTS
Text: No changes.

Version: 1.5.1
Date: 2015-10-20
Category: MODIFICATIONS
Text: No changes.

Version: 1.5.1
Date: 2015-10-20
Category: BUG FIXES
Text: Since the exemplary data have been imported with the bug which
        has been fixed in PAA version 1.3.3, all exemplary data sets
        have been reimported with the latest version of loadGPR() and
        saved as RData files. Now all exemplary data sets are complete.

Version: 1.3.3
Date: 2015-07-14
Category: GENERAL
Text: No changes.

Version: 1.3.3
Date: 2015-07-14
Category: NEW FEATURES
Text: No changes.

Version: 1.3.3
Date: 2015-07-14
Category: IMPROVEMENTS
Text: No changes.

Version: 1.3.3
Date: 2015-07-14
Category: MODIFICATIONS
Text: No changes.

Version: 1.3.3
Date: 2015-07-14
Category: BUG FIXES
Text: Bug in the function loadGPR() fixed (due to a wrong regular
        expression some data rows were not imported from gpr files in
        PAA versions 1.3.2 and 1.3.1 -> the bug was not relevant for
        the versions 1.3.0 and older).

Version: 1.3.2
Date: 2015-06-22
Category: GENERAL
Text: Update to the latest R version which has been released a few days
        ago (2015-06-18).

Version: 1.3.2
Date: 2015-06-22
Category: GENERAL
Text: Built with R-3.2.1

Version: 1.3.2
Date: 2015-06-22
Category: NEW FEATURES
Text: No changes.

Version: 1.3.2
Date: 2015-06-22
Category: IMPROVEMENTS
Text: No changes.

Version: 1.3.2
Date: 2015-06-22
Category: MODIFICATIONS
Text: NEWS file of version 1.3.1 corrected (wrong version number for
        the last update in the NEWS file).

Version: 1.3.2
Date: 2015-06-22
Category: BUG FIXES
Text: No changes.

Version: 1.3.1
Date: 2015-06-17
Category: GENERAL
Text: 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).

Version: 1.3.1
Date: 2015-06-17
Category: GENERAL
Text: Built with R-3.2.0

Version: 1.3.1
Date: 2015-06-17
Category: NEW FEATURES
Text: No changes.

Version: 1.3.1
Date: 2015-06-17
Category: IMPROVEMENTS
Text: 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.

Version: 1.3.1
Date: 2015-06-17
Category: MODIFICATIONS
Text: 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().

Version: 1.3.1
Date: 2015-06-17
Category: BUG FIXES
Text: 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.

Version: 1.1.1
Date: 2015-03-13
Category: GENERAL
Text: No changes.

Version: 1.1.1
Date: 2015-03-13
Category: NEW FEATURES
Text: No changes.

Version: 1.1.1
Date: 2015-03-13
Category: IMPROVEMENTS
Text: No changes.

Version: 1.1.1
Date: 2015-03-13
Category: MODIFICATIONS
Text: No changes.

Version: 1.1.1
Date: 2015-03-13
Category: BUG FIXES
Text: 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.

Version: 1.0.0
Date: 2014-10-13
Category: GENERAL
Text: First release version.

Version: 1.0.0
Date: 2014-10-13
Category: NEW FEATURES
Text: No changes.

Version: 1.0.0
Date: 2014-10-13
Category: IMPROVEMENTS
Text: No changes.

Version: 1.0.0
Date: 2014-10-13
Category: MODIFICATIONS
Text: No changes.

Version: 1.0.0
Date: 2014-10-13
Category: BUG FIXES
Text: No changes.

Version: 0.99.4
Date: 2014-10-03
Category: GENERAL
Text: First release version.

Version: 0.99.4
Date: 2014-10-03
Category: NEW FEATURES
Text: No changes.

Version: 0.99.4
Date: 2014-10-03
Category: IMPROVEMENTS
Text: No changes.

Version: 0.99.4
Date: 2014-10-03
Category: MODIFICATIONS
Text: No changes.

Version: 0.99.4
Date: 2014-10-03
Category: BUG FIXES
Text: Corrected \VignetteIndexEntry{} in the vignette Rnw file.

Version: 0.99.3
Date: 2014-10-02
Category: GENERAL
Text: License changed from GPL-3 to <93>BSD_3_clause + file LICENSE<94>
        due to license compatibility.

Version: 0.99.3
Date: 2014-10-02
Category: NEW FEATURES
Text: No changes.

Version: 0.99.3
Date: 2014-10-02
Category: IMPROVEMENTS
Text: Some dummy gpr files added to demonstrate loadGPR() in man pages
        and vignette.

Version: 0.99.3
Date: 2014-10-02
Category: IMPROVEMENTS
Text: First unit tests added.

Version: 0.99.3
Date: 2014-10-02
Category: IMPROVEMENTS
Text: Native routines registered.

Version: 0.99.3
Date: 2014-10-02
Category: IMPROVEMENTS
Text: Checking runtimes improved.

Version: 0.99.3
Date: 2014-10-02
Category: MODIFICATIONS
Text: No changes.

Version: 0.99.3
Date: 2014-10-02
Category: BUG FIXES
Text: Bug fixes in the vignette (e.g., \comment to \bioccomment).
        Missing vignette preambel added.

Version: 0.99.3
Date: 2014-10-02
Category: BUG FIXES
Text: Bug fixes in the code (e.g., max. line length of 80 characters
        ensured, "FALSE" instead of "F").

Version: 0.99.3
Date: 2014-10-02
Category: BUG FIXES
Text: Internal functions removed from export in the NAMESPACE.

Version: 0.99.2
Date: 2014-08-05
Category: GENERAL
Text: No changes.

Version: 0.99.2
Date: 2014-08-05
Category: NEW FEATURES
Text: No changes.

Version: 0.99.2
Date: 2014-08-05
Category: IMPROVEMENTS
Text: No changes.

Version: 0.99.2
Date: 2014-08-05
Category: MODIFICATIONS
Text: No changes.

Version: 0.99.2
Date: 2014-08-05
Category: BUG FIXES
Text: Minor change in the vignette (changing the
        selectFeatures()-option selection.method="rj.rfe"

Version: 0.99.2
Date: 2014-08-05
Category: to selection.method="rf.rfe" to make the code chunks runable
        on systems without Random Jungle installed
Text:

Version: 0.99.1
Date: 2014-08-05
Category: GENERAL
Text: No changes.

Version: 0.99.1
Date: 2014-08-05
Category: NEW FEATURES
Text: No changes.

Version: 0.99.1
Date: 2014-08-05
Category: IMPROVEMENTS
Text: No changes.

Version: 0.99.1
Date: 2014-08-05
Category: MODIFICATIONS
Text: No changes.

Version: 0.99.1
Date: 2014-08-05
Category: BUG FIXES
Text: Hard coded temp directory replaced by a tempdir()-based solution.

Version: 0.99.0
Date: 2014-08-03
Category: GENERAL
Text: NEWS file added.

Version: 0.99.0
Date: 2014-08-03
Category: GENERAL
Text: Vignette completed.

Version: 0.99.0
Date: 2014-08-03
Category: GENERAL
Text: Documentation completed.

Version: 0.99.0
Date: 2014-08-03
Category: GENERAL
Text: General compatibility for Windows, Mac OS X and Linux ensured.

Version: 0.99.0
Date: 2014-08-03
Category: NEW FEATURES
Text: No changes.

Version: 0.99.0
Date: 2014-08-03
Category: IMPROVEMENTS
Text: No changes.

Version: 0.99.0
Date: 2014-08-03
Category: MODIFICATIONS
Text: No changes.

Version: 0.99.0
Date: 2014-08-03
Category: BUG FIXES
Text: No changes.