Changes in 1.7.34 (2011-03-14)

  o added note on AffyComp results in the Vignette

Changes in 1.7.32 (2011-03-12)

SIGNIFICANT USER-VISIBLE CHANGES 

  o added estimation of probe affinities in rpa and RPA.pointestimate
  functions. Now returning expression values in the original data
  domain, i.e. in 'absolute' expression levels. Provides options for
  affinity estimation through affinity.method field in certain functions.
  o added 'affinity' field in rpa-class and rpa.list-class
  o added estimate.affinities function
  o removed exclude reference array option
  o added rpa.fit class (S3) to provide storage for an individual model
  o rpa.fit function now fits the model (including affinities) for
    given data. This is a generic function to calculate an individual
    model instance for any data following the distributional
    assumptions of the model. See tests/rpa.fit.test.R for an example. 

Changes in 1.7.3 (2011-01-20)

BUG FIXES

  o in 'rpa' wrapper function the exclude.reference.array option was
    interpreted in the opposite way than intended. Now the
    reference.control.array = TRUE excludes the reference array from
    output. Default is FALSE, i.e. reference array is included.

Changes in 1.7.2 (2011-01-14)

  o updated citation
  o moved license from GPL>=2 into FreeBSD since that is less
  restrictive open license. OK since all copyrights of the GPL>=2
  version are with the package author.

Changes in 1.5.2 (2010-05-19)

USER-VISIBLE CHANGES
  o the vignette has been improved
  o added firstlib.R function to print copyright notice during loading
  o added a copy of the GNU GPL 2 licence
  o added citation information, see citation("RPA")

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
