Changes in 1.3.6 (2010-03-28)

BUG FIXES
  o added documentation on 'get.probe.noise.estimates' function

Changes in 1.3.5 (2010-03-18)

USER-VISIBLE CHANGES

  o in the 'rpa' preprocessing wrapper, include the reference array
  (cind) to the differential gene expression matrix
  output. Optionally, the reference array can be excluded. See the
  'include.reference.array' parameter of function 'rpa'. Note that all
  differential expression values of the reference array are 0 since
  the reference is compared against itself.

  o added function get.probe.noise.estimates. Outputs probe-level
  noise estimates with normalization options.

BUG FIXES

  o added destructive=TRUE into background correction. Should help with
  large data.


Changes in 1.3.2 (2010-03-02)

SIGNIFICANT USER-VISIBLE CHANGES

  o changed default sigma2.method into 'robust'

  o control array default set to cind = 1 (previosly sampled at
  random if not specified)

  o initialize.priors replaced by set.priors function


USER-VISIBLE CHANGES

  o removed sigma2.guess from user-defined parameters in RPA.iteration

  o RPA.pointestimate: added regularization parameters alpha, beta


NEW FEATURES

  o support for alternative CDF files

  o rpa function: a wrapper for preprocessing gene expression data
  with the RPA model

  o rpa.plot function: visualize probe-level data and results for a
  given probeset

  o background correction to RPA.preprocess

  o option to define background correction and normalization
  parameters

  o regularization for noise term estimation (sigma2)

  o sigma2.method 'mean' and 'robust' added


BUG FIXES

  o rpa class: added elements 'data', 'cdf' and 'abatch'

  o RPA.preprocess: background correction added, and log2
  transformation now done after normalization

  o added 'maxloop' parameter to RPA.iteration function call 

  o moved the contents of R/zzz.R into AllGenerics.R, AllClasses.R,
  *-methods.R, *-accessors.R

  o code optimized for speed
