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>