NEWS
PAA 1.7.1 (2016-05-13)
GENERAL
- Built with the latest R version (R-3.2.4 Revised).
- Built with the latest Rtools version (Rtools 3.3).
- Update of the PAA citation: PAA applications note, Turewicz et al.,
Bioinformatics, 2016, PMID: 26803161, added to the CITATION
file.
- Update of the URL in the DESCTIPTION file.
- Correction of some typos in the documentation.
- Update of the vignette to demonstrate the new features.
NEW FEATURES
- New function: batchFilter.anova() for multi-batch scenarios.
- New function: plotFeaturesHeatmap.2() as an alternative to
plotFeaturesHeatmap().
- 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.
- Now the customized object classes EListRaw and EList contain the
new component "array.type" added by loadGPR when the data is
imported.
IMPROVEMENTS
- Additional and more informative error messages added.
- The function plotArray() is more flexible. Now, not only
ProtoArrays can be plotted. Moreover, now the plot can be saved
also as png file.
MODIFICATIONS
- The loadGPR() and plotArray()-argument "protoarray.aggregation" has
been renamed to "aggregation" and the default value has been
changed to "none".
- The loadGPR() argument "array.type" is mandatory now.
BUG FIXES
- Plots created during rlm normalization by normalizeArrays() were in
logE scale and not in log2 scale. This has been fixed.
- Correction of regular expressions for rlm normalization in
normalizeArrays() and for data import in loadGPR().
PAA 1.5.1 (2015-10-20)
GENERAL
NEW FEATURES
- 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.
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
- 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.
PAA 1.3.3 (2015-07-14)
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
- 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).
PAA 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
IMPROVEMENTS
MODIFICATIONS
- NEWS file of version 1.3.1 corrected (wrong version number for the last update in the
NEWS file).
BUG FIXES
PAA 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
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.
PAA 1.1.1 (2015-03-13)
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
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.
PAA 1.0.0 (2014-10-13)
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
PAA 0.99.4 (2014-10-03)
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
- Corrected \VignetteIndexEntry{} in the vignette Rnw file.
PAA 0.99.3 (2014-10-02)
GENERAL
- License changed from GPL-3 to 93BSD_3_clause + file LICENSE94 due to license compatibility.
NEW FEATURES
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
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.
PAA 0.99.2 (2014-08-05)
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
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
PAA 0.99.1 (2014-08-05)
GENERAL
NEW FEATURES
IMPROVEMENTS
MODIFICATIONS
BUG FIXES
- Hard coded temp directory replaced by a tempdir()-based solution.
PAA 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
IMPROVEMENTS
MODIFICATIONS
BUG FIXES