2009-12-01  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* rel2_5 branch: dyebias.application.subset now returns a matrix of
	logicals (as advertised), rather than a matrix of 0's and 1's.

	* rel2_5 branch: fixed critical bug in
	plotfunctions.R:.merge.dyebias() (now using
	maLabels(maGnames)). Also re-created the vignette.

2009-08-28  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* improved error/info messages
	* added p.value  to output of dyebias.estimate.iGSDBs
	* avoiding factors in data.frames
	* dyebias.apply.correction now also returns the uncorrected data for convenience
	* small changes to the vignette text. 
	* version bumped to 1.3.3

2009-04-22  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* now using median of ratios, not ratio of medians. Small changes
	in the correction object returned by dyebias.apply.correction: the
	correction$summary data.frame no longer has {green,red}.bias
	columns; the correction$estimators list now additionally has
	{green,red}.iGSDBs. 
	* 'release' 1.3.1

2009-04-01  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* all example()s now non-verbose; adjustments to vignette
	* release 1.0.6

2009-03-19  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* various little fixes
	* release 1.0.5

2009-03-12  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* default is.balanced argument in dyebias.estimate.iGSDBs is now
	consistently TRUE in both docs and code
	* version 1.04

2009-03-04  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* half of the vignetta is now eval=FALSE, since it takes too
	long to create the PDF file
	* version 1.0.3

2009-02-27  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* version 1.0.2
	
	* misc. changes/clarifications to documentation

	* dyebias.monotonicityplot now also in vignette
	
	* put under GPL v3

2009-02-25  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* added dyebias.monotonicity and dyebias.monotonicityplot

2009-02-17  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* version 1.0.1

2009-02-12  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* plotfunctions.R: added type argument to dyebias.trendplot

2009-02-10  Philip Lijnzaad  <p.lijnzaad@med.uu.nl>

	* dyebias.Rnw: misc. editorial changes
	
