Package: aroma.light
====================

Version: 1.21.2 [2011-10-10]
o Updated robustSmoothSpline() such that it works with the new
  "uniqueness" scheme of smooth.spline() in R v2.14.0 and newer.
  It is tricky, because robustSmoothSpline() is a reiterative 
  algorithm which requires that the choosen "unique" x:s does
  not change in each iteration.  Previously, 'signif(x, 6)' was
  used to identify unique x:s, which gives the same set of values
  when called twice, whereas this is not true for the new choice
  with 'round((x - mean(x))/tol)'.


Version: 1.21.1 [2011-06-26]
o Added argument 'aspectRatio' to plotMvsA().  It can be used to adjust
  the range of the 'Mlim' argument relative to the 'Alim' argument.


Version: 1.21.0 [2011-04-13]
o The version number was bumped for the Bioconductor devel version.


Version: 1.20.0 [2010-04-13]
o The version number was bumped for the Bioconductor release version.


Version: 1.19.6 [2011-04-12]
o CLEANUP: Removed internal patch of principal.curve().  If an older
  version than princurve v1.1-10 is used, an informative error is
  thrown requesting an update.  The internal patch is part of the
  offical princurve v1.1-10 release (since 2009-10-04).
o Now all methods allocate objects with NAs of the appropriate mode.
o KNOWN ISSUES: Recent updates to smooth.spline() in R v2.14.0 
  causes robustSmoothSpline() to break in some cases.


Version: 1.19.5 [2011-04-08]
o Now weightedMedian() returns NA:s of the same mode as argument 'x'.


Version: 1.19.4 [2011-03-03]
o Same updates as in v1.18.4.


Version: 1.19.3 [2011-02-05]
o Same updates as in v1.18.3.


Version: 1.19.2 [2010-10-22]
o Same updates as in v1.18.2.


Version: 1.19.1 [2010-10-18]
o Same updates as in v1.18.1.


Version: 1.19.0 [2010-10-18]
o The version number was bumped for the Bioconductor devel version.


Version: 1.18.4 [2011-03-03]
o BUG FIX: findPeaksAndValleys(x, to) were 'x' is numeric would use
  partial match and interpret 'to' as argument 'tol' and not part of
  '...' passed to density().  This problem was solved by placing '...'
  before argument 'tol'.  Thanks Oscar Rueda at the Cancer Reasearch UK
  for reporting on and identifying this bug.


Version: 1.18.3 [2011-02-05]
o DOCUMENTATION: Added paragraphs on how to do affine normalization 
  when channel offsets are known/zero.  Same for multiscan calibration
  when scanner offsets are known/zero.
o DOCUMENTATION: Fixed broken links to help for iwpca().


Version: 1.18.2 [2010-10-22]
o DOCUMENTATION: Minor clarifications to the help page on
  "1. Calibration and Normalization".  This page is now also
  referenced in help("calibrateMultiscan").


Version: 1.18.1 [2010-10-18]
o These updates were supposed to be in v1.17.7, but we forgot
  to commit them to the BioC repository before the new BioC release.
o Argument 'censorAt' for fitNaiveGenotypes() has new default.
o BUG FIX: fitNaiveGenotypes(..., subsetToFit=<logical>) would throw
  an exception reporting "Some elements of argument 'subsetToFit' is 
  out of range ...".


Version: 1.18.0 [2010-10-18]
o The version number was bumped for the Bioconductor release version.


Version: 1.17.6 [2010-10-08]
o Now findPeaksAndValleys() returns a object of class PeaksAndValleys,
  which extends data.frame.


Version: 1.17.5 [2010-10-07]
o Added optional argument 'fit' to callNaiveGenotypes() for passing
  a model fit returned by fitNaiveGenotypes().  If not specified,
  callNaiveGenotypes() will call fitNaiveGenotypes() internally.
o Added fitNaiveGenotypes(), which previously was only internal
  of callNaiveGenotypes().


Version: 1.17.4 [2010-10-06]
o Added findPeaksAndValleys() for the 'density' class, which then
  findPeaksAndValleys() for 'numeric' utilizes.


Version: 1.17.3 [2010-09-18]
o ROBUSTNESS: Now normalizeFragmentLength() asserts that arguments
  'fragmentLengths' and 'y' contain at least some finite values and 
  specifies the same number of units.  In addition, the method also
  gives more informative error messages in case it cannot fit the
  normalization function due to non-finite values.


Version: 1.17.2 [2010-08-04]
o Added argument 'preserveScale' to normalizeTumorBoost() to
  rescale the calibrated allele B fractions for heterozygous SNPs
  such that the compression relative to the homozgygotes is
  preserved.


Version: 1.17.1 [2010-07-23]
o Same updates as in release version v1.16.1.


Version: 1.17.0 [2010-04-22]
o The version number was bumped for the Bioconductor devel version.


Version: 1.16.1 [2010-07-23]
o Now callNaiveGenotypes() returns the model estimates as attribute
  'modelFit'.  This feature was supposed to be in v1.16.0.


Version: 1.16.0 [2010-04-22]
o The version number was bumped for the Bioconductor release version.


Version: 1.15.4 [2010-04-08]
o R devel assumes ASCII encoding unless specified. Added explicit
  Latin-1 encoding to the DESCRIPTION file to R CMD check to pass.


Version: 1.15.3 [2010-04-04]
o Added normalizeDifferencesToAverage(), normalizeTumorBoost(), 
  callNaiveGenotypes() and internal findPeaksAndValleys(),
  which all were moved from the aroma.cn package.


Version: 1.15.2 [2010-03-12]
o BUG FIX: The example of fitPrincipalCurve() used a non-existing
  argument name in the calls to substitute().  Thanks to Brian
  Ripley at University of Oxford for reporting this.


Version: 1.15.1 [2009-11-01]
o Now fitPrincipalCurve() only uses the internal bug-fix patch
  if a version earlier than princurve v1.1-10 is installed.


Version: 1.15.0 [2009-10-27]
o The version number was bumped for the Bioconductor devel version.


Version: 1.14.0 [2009-10-27]
o The version number was bumped for the Bioconductor release version.


Version: 1.13.6 [2009-10-20]
o FIX: CITATION file reverted to that of v1.13.4.


Version: 1.13.5 [2009-10-08]
o CITATION file [incorrectly] updated by BioC maintainers.


Version: 1.13.4 [2009-09-23]
o Fixed a few broken Rd links.


Version: 1.13.3 [2009-07-15]
o ADDED: fit- and backtransformXYCurve().
o Added attribute 'processingTime' to the fit object returned 
  by fitPrincipalCurve().


Version: 1.13.2 [2009-05-29]
o Incorporating the same updates as in release v1.12.2.


Version: 1.13.1 [2009-05-13]
o Incorporating the same updates as in release v1.12.1.


Version: 1.13.0 [2009-04-20]
o The version number was bumped for the Bioconductor devel version.


Version: 1.12.2 [2009-05-29]
o Replacing old HOWTOCITE with a standard CITATION file.
o BUG FIX: Previous bug fix in backtransformPrincipalCurve() regarding
  argument 'dimension' broke the initial purpose of this argument. Since
  both use cases are still of interest, how the subsetting is done is now
  based on whether the number of dimensions of the input data and the 
  model fit match or not. See help and example code for 
  'backtransformPrincipalCurve.matrix'.


Version: 1.12.1 [2009-05-13]
o BUG FIX: backtransformPrincipalCurve(..., dimensions) did not subset
  the 'X' matrix. Also, the method now returns a matrix of the same
  number of columns requested.  The Rd example now illustrates this.
  Thanks to Pierre Neuvial, UC Berkeley for the troublshooting and fix.


Version: 1.12.0 [2009-04-20]
o The version number was bumped for the Bioconductor release version.


Version: 1.11.2 [2009-02-08]
o BUG FIX: An error was thrown in backtransformPrincipalCurve() 
  when argument 'dimensions' was specified.


Version: 1.11.1 [2009-01-12]
o Added fit- & backtransformPrincipalCurve().


Version: 1.11.0 [2008-10-21]
o The version number was bumped for the Bioconductor devel version.


Version: 1.10.0 [2008-10-21]
o The version number was bumped for the Bioconductor release version.


Version: 1.9.2 [2008-09-11]
o Added argument 'onMissing' to normalizeFragmentLength() for specifying
  how to normalize (if at all) data points for which the fragment lengths 
  are unknown.  For backward compatibility, we start off by having it
  "ignore" by default.
o MEMORY OPTIMIZATION: robustSmoothSpline() is now cleaning out
  more variables when no longer needed.


Version: 1.9.1 [2008-05-10]
o Incorporating the same updates as in release v1.8.1.


Version: 1.9.0 [2008-04-29]
o The version number was bumped for the Bioconductor devel version.


Version: 1.8.1 [2008-05-10]
o BUG FIX: If the 'subsetToFit' of normalizeFragmentLength() was 
  shorter than the number of data points, an exception was thrown.
  The test was supposed to assert that the subset was not greater
  than the number of data points.


Version: 1.8.0 [2008-04-29]
o The version number was bumped for the Bioconductor release version.


Version: 1.7.2 [2008-04-14]
o Added normalizeFragmentLength().
o Added normalizeQuantileSpline().
o Renamed normalizeQuantile() to normalizeQuantileRank().
o Added plotXYCurve().
o Added predict() for the 'lowess' class.


Version: 1.7.1 [2007-11-28]
o The startup message when loading the package is generated with
  packageStartupMessage() so that it can be suppressed.
o Package now only suggest the R.oo package, and instead depends
  on the new R.methodsS3.
o TYPO: Corrected a spelling error in the help pages.
o Package passes R CMD check R v2.6.1.


Version: 1.7.0 [2007-10-08]
o The version number was bumped for the Bioconductor devel version.


Version: 1.6.0 [2007-10-08]
o The version number was bumped for the Bioconductor release version.


Version: 1.5.2 [2007-08-10]
o Package pass R CMD check R v2.6.0.


Version: 1.5.1 [2007-06-08] (this was mistakenly versioned 1.4.1)
o Added normalizeAverage().
o Package pass R CMD check R v2.6.0 with Rd encoding errors.


Version: 1.5.0 [2007-05-09]
o The version number was bumped for the Bioconductor devel version.


Version: 1.4.0 [2007-05-09]
o The version number was bumped up with the Bioconductor release.


Version: 1.3.1 [2007-01-15]
o Removed code to use 'modreg' for backward compatibility with R < 1.9.0.
o Added R.utils to Suggests field of DESCRIPTION.


Version: 1.3.0 [2006-10-??]
o The devel version number was bumped up with the Bioconductor release.


Version: 1.2.0 [2006-10-03]
o The version number was bumped up with the Bioconductor release.


Version: 1.1.0 [2006-07-20]
o Added to Bioconductor v1.9.
o Added some trial RSP pages. Try browseRsp() in the R.rsp package.


Version: 0.1.7 [2006-06-27]
o Made the package truely standalone except from R.oo.  Previously package
  R.basic was used in some of the examples.


Version: 0.1.6 [2006-05-22]
o Added a namespace for the package.
o Added 'biocViews' since the package will eventually be added 
  to the Bioconductor project.
o Added medianPolish() which is much faster than stats::medpolish()
  when there are no NA.
o Added plotDensity() for list of vectors as well as for matrices.
o Added normalizeQuantile() for lists of vectors as well as for a
  single vector of numerics.  To calculate the target quantile there
  is a new function averageQuantile(), which is also for lists of 
  vectors.  It latter does not support robust estimatation of the 
  average, because it safes memory.
o Updated normalizeQuantile() for matrices according to the updates
  in the limma package.


Version: 0.1.5 [2006-04-21]
o Minor speedup to weightedMedian(), e.g. negative weights do no longer give
  and error, but are treated as zero instead.  This removes some overhead
  of the function.  Also, if it is known that there are no NAs that can be
  specified by na.rm=NA, which will skip NA checks.


Version: 0.1.4 [2006-03-28]
o Updated broken Rd links.
o Updated the references to publications.


Version: 0.1.3 [2006-01-22]
o Added help on the returned parameters of fitIWPCA().
o Now fitIWPCA() does not return the data matrix. This is to save memory.
  The calling algorithm can equally well add the data if it is needed.


Version: 0.1.2 [2005-09-06]
o All plot methods displaying log-ratios now assures that no fake
  log-ratios are calculated due to two negative raw signals.  
  Similarily, methods display log-intensities now assures that the
  log-intensities are calculated as doubles to avoid possible 
  overflow warnings for too large integers.


Version: 0.1.1 [2005-07-26]
o Added sampleCorrelations() and sampleTuples().
o Now argument 'interpolate' of weightedMedian() defaults to TRUE only 
  if 'ties' is NULL.


Version: 0.1.0 [2005-06-03]
o Created. Most of the matrix methods were copied from the R.basic 
  and the aroma packages. The purpose of this package is to provide
  a standalone package, which does not require any of the aroma
  classes. This will allow the methods to be used by end users as
  is, or be utilized in other packages.
