2010-10-04  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* dyebias-vignette.Rnw: editorial changes in vignette; rebuilt the
	dyebiasCompleteVignette.pdf from it (v. 1.7.8)

2010-09-02  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* dyebias.R (dyebias.estimate.iGSDBs): In unbalanced design,
	reference cannot be NULL or ''. Also editorial changes in man
	pages and vignette, which has been recompiled (v.1.7.6). 
	

2010-09-01  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* dyebias.R (dyebias.apply.correction): more robust handling of
	summary information. (v.1.7.5)

2010-08-30  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* dyebias.R (dyebias.estimate.iGSDBs): bug in error message (v1.7.4)

	* Fixed typo and clarified docu on reference argument to function
	dyebias.estimate.iGSDBs (v1.7.2, v1.7.3)

2010-05-26  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* Added dyebias-package.Rd help file (auto-generated from
	DESCRIPTION). DESCRIPTION.Description more elaborate now. More
	precise error reporting in .find.estimators (v1.7.1)

2010-02-26  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* Small change to vignette.

2010-01-27  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* Applied bug fixes sent by Guido Hooiveld: errors in
	.set.design(), due to having factors (rathern than strings)
	in the maInfo(maTargets(data)) data.frame. Also a bug in the code
	checking the design; replaced and extended. Both bugs only affected
	the fairly uncommon unbalanced set-of-references designs.
	In addition, clarified the dye (unswapping) in the vignette.
	(v1.5.8)

2009-12-07  Philip Lijnzaad  <p.lijnzaad@umcutrecht.nl>

	* added gassco.pdf, high-level description of the method, and
	application to tumor data. (v1.5.7)

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

	* renamed vignette for clarity Inserted extrablurp at
	top of vignette to warn of incompleteness (v1.5.6).

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

	* Adjusted documentation to get rid of some overfull
	hboxes. Replaced the 'submitted' reference with actual one. (v1.5.5)

	* Now using stringsAsFactors=FALSE for each and every data.frame()
	call (v1.5.4)

        * Added .check.reporter.labels and .check.slide.labels. Clarified
	documentation and error messages. Data frame returned from
	dyebias.estimate.iGSDBs now always contains a column p.value,
	filled with NA's if not calculated.  (v1.5.3)

	* trunk: merged rel2_5 fixes.  (v1.5.2)

	* rel2_5 branch: dyebias.application.subset now returns a matrix of
	logicals (as advertised), rather than a matrix of 0's and 1's. (v1.5.1)

	* 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
	
