CHANGES IN VERSION 1.1.8
------------------------
 o semi-sup and sup comparison sections in ml vig <2013-10-09 Wed>

CHANGES IN VERSION 1.1.7
------------------------
 o getMarkers has names arg <2013-10-01 Tue>

CHANGES IN VERSION 1.1.6
------------------------
 o new outliers arg to plot2D <2013-09-23 Mon>
 o cite addMarkers in vignette <2013-09-26 Thu>
 o add code chunk in poster vig <2013-09-26 Thu>

CHANGES IN VERSION 1.1.5
------------------------
 o added biocViews <2013-09-19 Thu>
 o added knitr vig engine in ml <2013-09-19 Thu>
 o import dependencies <2013-09-20 Fri>

CHANGES IN VERSION 1.1.4
------------------------
 o building ml vignette in Makefile <2013-09-11 Wed>

CHANGES IN VERSION 1.1.3
------------------------
 o new private anyUnknown function, used in phenoDisco, to check 
   for the presence of unlabelled ('unknown') data <2013-08-27 Tue>
 o added a note in vignette about "unknown" convention to define 
   protein with unknown localisation <2013-08-28 Wed>
 o Added HUPO 2011 poster <2013-09-09 Mon>

CHANGES IN VERSION 1.1.2
------------------------
 o fixed Author[s]@R <2013-05-16 Thu>
 o na.rm=TRUE in f1Count <2013-05-19 Sun>
 o added CITATION file <2013-06-07 Fri>
 o new testMarkers function <2013-06-29 Sat>
 o error message in getBestParams suggests to use testMarkers <2013-06-29 Sat>
 o nndist methods (see issue #23) <2013-07-01 Mon>
 o remove unnecessary as.matrix in plot2D's cmdscale <2013-07-19 Fri>
 o added plot2D(..., method = "MDS") example <2013-07-19 Fri>
 o changed 'euclidian' to 'euclidean' in nndist_matrix <2013-07-26 Fri>
 o fixed row ordering in phenoDisco, input and output rownames are now the same <2013-08-13 Tue>
 o Using filterNA in phenoDisco <2013-08-13 Tue>

CHANGES IN VERSION 1.1.1
------------------------
 o Update README.md to reflect availability in stable release 
   and biocLite installation <2013-04-07 Sun>
 o new MSe pipeline <2013-04-07 Sun>
 o perTurbo using Rcpp <2013-04-16 Tue>
 o initial clustering infrastructure (not exported) <2013-04-17 Wed>
 o new markerSet function <2013-04-24 Wed>
 o plsaOptim's ncomp is now 2:6 <2013-04-27 Sat>
 o added forword to vignette <2013-04-29 Mon>
 o default k is now seq(3, 15, 2) in knnOptim <2013-05-09 Thu>

CHANGES IN VERSION 1.1.0
------------------------
 o Bioc 2.13 devel version bump

CHANGES IN VERSION 1.0.0
------------------------
 o Bioc 2.12 stable version bump

CHANGES IN VERSION 0.99.17
--------------------------
 o illustrating class.weights in the 
   vignette <2013-03-24 Sun>

CHANGES IN VERSION 0.99.16
--------------------------
 o new addMarkers function <2013-03-22 Fri>

CHANGES IN VERSION 0.99.15
--------------------------
 o Fixing issues in vignette <2013-03-22 Fri>

CHANGES IN VERSION 0.99.14
--------------------------
 o Added scale in tutorial <2013-03-02 Sat>
 o implemented viction <2013-03-09 Sat>
 o New vignette section on phenoDisco follow 
   up classification <2013-03-19 Tue>
 o Using knitr engine <2013-03-19 Tue>

CHANGES IN VERSION 0.99.13
--------------------------
 o depending on MSnbase >= 1.7.23 as makeNaData 
   needs MSnbase:::nologging <2013-02-27 Wed>
 o updated phenoDisco parameters, added error messages when an 
   insufficient number of markers per class and/or number of
   classes are used and updated phenoDisco help file <2012-02-28 Thu>
 o added first belief diffscores function <2013-03-01 Fri>

CHANGES IN VERSION 0.99.12
--------------------------
 o plot2D has gained a plot argument <2013-02-19 Tue>
 o new f1Count method <2013-02-20 Wed>
 o new makeNaData function <2013-02-20 Wed>
 o new makeNaData2 function <2013-02-21 Thu>
 o new whichNAfunction <2013-02-20 Wed>
 o updated tutorial vignette <2013-02-20 Wed>
 o Now passing ... to predictor functions in 
   xxxClassification (reported by Marianne Sandin) <2013-02-26 Tue>

CHANGES IN VERSION 0.99.11
--------------------------
 o setUnknowncol(NULL) and friedns reset to default 
   values <2013-02-19 Tue>

CHANGES IN VERSION 0.99.10
--------------------------
 o new default col/pch setters <2013-02-16 Sat>

CHANGES IN VERSION 0.99.9
-------------------------
 o Updates to phenoDisco: verbose param, fixed error in example, 
   adding params to processingInfo <2013-02-11 Mon> 
 o Unexported getOtherParams method <2013-02-12 Tue>
 o adding export param documentation <2013-02-12 Tue>

CHANGES IN VERSION 0.99.8
-------------------------
 o Integration of the perTurbo algorithms, contributed 
   by Thomas Burger and Samuel Wieczorek <2013-01-18 Fri>
 o summariseMatList now has na.rm = TRUE by default <2013-01-19 Sat>
 o PerTurbo's inv/reg now as other hyperparams <2013-02-11 Mon>

CHANGES IN VERSION 0.99.7
-------------------------
 o knitr 1.0 compatibility <2013-01-15 Tue>
 o Updated phenoDisco documentation and README <2013-01-10 Thu>

CHANGES IN VERSION 0.99.6
-------------------------
 o removed updateClass man <2013-01-03 Thu>
 o removed old Rd files <2013-01-03 Thu>
 o Deprecating *Regularisation and *Prediction function <2013-01-03 Thu>
 o Updated new names in test_ml.R <2013-01-04 Fri>

CHANGES IN VERSION 0.99.5
-------------------------
 o more reg data into GenRegRes objects 
   - cmMatrices (knn) <2012-11-15 Thu> (other) <2012-11-30 Fri>
   - testPartitions (knn) <2012-11-17 Sat> (other) <2012-11-30 Fri>
 o new minMarkers function <2012-11-16 Fri>
 o renamed updateClass to minClassScore <2012-11-16 Fri>
 o renamed xxxRegularisation to xxxOptimisation <2012-11-30 Fri>
 o renamed xxxPrediction to xxxClassification <2012-11-30 Fri>
 o renamed getRegularisedParams to getParams <2012-11-30 Fri>
 o moved exprsToRatios to MSnbase <2012-12-05 Wed>
 o updated phenoDisco help file <2012-12-07 Fri>
 o updated phenoDisco code to cope with identical protein profiles <2012-12-07 Fri>

CHANGES IN VERSION 0.99.4
-------------------------
 o Adding README file describing Rd generation
   and suggesting roxygen2 <2012-11-14 Wed>
 o Added scol=NULL to ignore completely <2012-11-14 Wed>

CHANGES IN VERSION 0.99.3
-------------------------
 o pdres in extdata - updated vignette <2012-11-14 Wed>
 o udpated pd's GS/times default <2012-11-14 Wed>

CHANGES IN VERSION 0.99.2
-------------------------
 o fixed MLearn("formula", "MSnSet", "clusteringSchema", 
   "missing") - interface was wrong <2012-11-10 Sat>
 o vignette updates <2012-11-10 Sat> <2012-11-11 Sun>
 o nicer knn score names when scores = "all" <2012-11-11 Sun>

CHANGES IN VERSION 0.99.1
-------------------------
 o updated exprsToRatio when ncol(object) is 2 <2012-11-05 Mon>
 o typos in vignette <2012-11-09 Fri> <2012-11-10 Sat>
 o new MLearn method for signature 
   c("formula", "MSnSet", "clusteringSchema", "missing") <2012-11-09 Fri>
 o Several vignette udpates <2012-11-10 Sat>

CHANGES IN VERSION 0.99.0
-------------------------
 o Submission to Bioc <2012-11-04 Sun>
