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

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.
