Package: codelink
====================

Version 1.23.2

o Improvements on how codPlotScatter() manages labels. Renamed generic scatter plot function plotma() to plotxy(), which better reflects the current status.

Version 1.23.1

o Implemented missing function codPlotScatter() for CodelinkSet objects (accessible via codPlot(..., what = "scatter")). The implementation reuses the plotma()
  function used by codPlotMA(). By default the first array is plotted against the median. Thanks to William Michels for reporting this and testing the CodelinkSet
  framework.

o Minor improvements to linear model section in CodelinkSet-vignette. Now the code is evaluated.

Version 1.15.4

o Fixed check fail in windows machine by putting "multicore" in Enhancements, and checking if function "mclapply" is loaded. Addapted documentation to 
explain the new behavior.

Version 1.15.3

o Added missing file (averageProbes.Rd) to the svn.

Version 1.15.2

o Added CodelinkSetUnique class to store objects with unique probes. These objects use as featureNames the probe ID, and
  hence should be compatible with other packages that make use of featureNames() and the annotation packages.
  
o Added function averageProbes() that computes the average of duplicated probes in the array. Currently is does the mean(). The
  standard deviation is computed too and stored in the slot "sd" (no accessor method at the moment). This computation requires
  time and therefore a call to mclapply() in multicore package is implemented through the optional argument 'parallel' (FALSE by
  default). Use of 'parallel = TRUE' is not recommended on GUI (like the Cocoa R.app) (see multicore package for issues with this). 

Version 1.15.1

o Added '...' to readCodelinkSet() so that it pass additional arguments (e.g. 'flag') to readCodelink(). Thank you to Luca Beltrame for the suggestion and patch.
o Now when readCodelinkSet() reads a list of files and the phenoData is not supplied it will create a default one, instead of failing.

Version: 1.15.0

o Version number bumped for BioC devel branch.

Version: 1.13.6

o Fixed bug in codCorrect() that would prevent the methods "half" and "subtract" for being available. Thanks to FrŽdŽric Boyer for reporting this.

Version: 1.13.5

o Fixed warnings about missing (or suspect) links in documentation. Added tem-
  plate man page for CodelinkSet class.

Version: 1.13.4

o Fixed warning on R CMD check about mismatch between objects and documentation.
