CHANGES IN VERSION 1.19.1
-------------------------
 - Fix error in subsetIBSpectra and exclude and namespace imports
  (Laurent Gatto <2016-10-07 Fri>)

CHANGES IN VERSION 1.17.1
-------------------------
 - Fixed critical bug in isotope impurity correction method. 
   Isobar used a transposed matrix for isotope impurity correction prior to this fix.
   Quantification results will change when isotope impurity correction is performed
   Bug discovered by Dario Strbenac https://support.bioconductor.org/p/74301/#79900).

CHANGES IN VERSION 1.16.0
-------------------------
 - Bioconductor release 3.2

 CHANGES IN VERSION 1.14.0
 -------------------------
  - Bioconductor release 3.1

CHANGES IN VERSION 1.13.0
-------------------------
 - calcCumulativeProbXGreaterThanY() contributed by A. Stukalov, for calculating cummulative p-values with replicates
 - Bioconductor version increment

CHANGES IN VERSION 1.12.0
-------------------------
 - Bioconductor release 3.0

 CHANGES IN VERSION 1.10.0
 -------------------------
  - Bioconductor release 2.9

CHANGES IN VERSION 1.9.5
------------------------
 - FIX FOR TMT-10plex tags: previous version had wrong annotation of N and C for 127,128,129,130
 - Speed improvements for p-value calculation by vectorization, contributed by A. Stukalov

CHANGES IN VERSION 1.9.3
------------------------
 - allow the use of a combination matrix in NoiseModel reporterTagNames
 - added function getProteinInfoFromTheInternet which automatically recognizes Uniprot and Entrez ACs. Set now as default 'protein.info.f' in the report configuration.
 - Overhauled isobar-analysis.Rnw
   - use of ltxtables to allow optimal column widths (longer runtime, however)
   - use [[ instead of $  for accession of lists
   - better column and grouping description
 - allow report generation without a proteinInfo object
 - set report cache directory to 'cache' (instead of '.') by default
 - 1.9.3.2:
   - mascotParser2.pl: allow to skip modif-conversion with -no-modiconv
   - mascotParser2.pl: set --lightXML as default
   - report generation: set combn.method="versus.channel", which computes the ratios against the first channel
   - various PDF report improvements
 - 1.9.3.3:
   - report tables are written into tables which are loaded with LTxtable
      report generation takes longer now
   - fixes in correct.peptide.ratios
     - use combined protein group for peptide-protein mapping
     - use only reporter proteins for mapping
   - fix in creation of protein groups from template,
      subset by peptide _and_ modif

CHANGES IN VERSION 1.9.2
------------------------
 - fix issue of NA in 'n.spectra' when calculating summarized ratios
 - various report improvements:
   - use column of variable width to display class labels
   - add attributes of quant table to summarized result table
   - improved placement of tikz peptide group pictures

CHANGES IN VERSION 1.7.6
------------------------
 - added TMT 10plex (contribution from Florent Gluck)
 - fixed bugs with system.file not working on R < 2.11 (contribution from Florent Gluck)
 - fixed bug in isobar-qc which was not working without normalize=TRUE
 - added writeHscoreData for usage with Hscorer.py (MM Savitski, 2010)
 - shQuote commands correctly - should fix issues running report generation on Windows
 - added calculations and XLS tab for peptides with unsure localization of the modification site
 - updated scripts for creating multi-sample reports (create.meta.reports)

CHANGES IN VERSION 1.7.5
------------------------
 - fixed critical bugs: Excel report output had wrong ordering, ie ratios did
   not correspond to the meta information [introduced in version 1.7.3].
 - fix of real peptide names: Reexport I/L peptides in reports

CHANGES IN VERSION 1.7.4
------------------------
 - improved MSGF+ search result import
 - refactored report properties: all properties can now be defined in 
    in the properties.R
 - speed and memory usage improvements when creating wide XLS report
 - ratio p-value adjustment now works per comparision instead of globally

CHANGES IN VERSION 1.7.3
------------------------
 - fix wide XLS report format
 - novel plot for ratio combinations in QC report
    showing individual ratio distributions and 
    significant ratios

CHANGES IN VERSION 1.7.2
------------------------
 - added TMT 6plex masses to phosphoRS export script
 - fixed mascot parsers
 - MzIdentML version  1.1.0 support implemented [not fully tested]

CHANGES IN VERSION 1.7.1
------------------------
 - fixed import of MzIdentML files from Mascot and ProteomeDiscoverer

CHANGES IN VERSION 1.6.0
------------------------
 - added modules and functions for PTM quantification

CHANGES IN VERSION 1.5.3
------------------------
 - parallelization support! Set options(isobar.parallel=TRUE) and 
   register a cluster using registerDoMC or registerDoSNOW.
   Used when creating ratio tables.


CHANGES IN VERSION 1.5.2
------------------------
 - added MSGF+ tsv import [one-line-per-psm format]
 - refactored various parts of the code (proteinRatios, report-utils, isobar-import)
 - PTM XLS report: report significance for protein ratio, and peptide ratio

CHANGES IN VERSION 1.5.1
------------------------
 - added molecular weight correction to emPAI and dNSAF
 - added property 'ratiodistr.class.labels': biological variability can be 
   calculated in the report with other labels
 - improved PDF analysis report: added number of proteins in each section
 - added location scale family T distribution as biological variability
   distribution (distr class) and fitTlsd.
 - better protein PDF analysis report layout.

CHANGES IN VERSION 1.5
------------------------
 - Added modules for PTM validation and quantification
   - Validation
     - PhosphoRS XML import writers and outpout readers
     - DeltaScore calculation when the data is provided
   - Quantification
     - All quantifications can be done now either on the protein level,
       peptide level, or modified peptide level. For modified peptide level,
       supply a matrix with a 'peptide' and 'modif' column to the 
       appropriate functions.
     - Correction of peptide ratios with protein ratios is possible. Also
       the variance can be adjusted (assuming no or full correlation)
   - Report generation
     - Import PhosphoSitePlus or neXtProt information on modification sites

CHANGES IN VERSION 1.3.0
------------------------
 - Rockerbox import (just define the XXX.dat.peptides.csv as identifications)
 - possibility to define columns for XLS report in properties.R. e.g.
   xls.report.columns <- c("ratio","is.significant",
                           "ratio.minus.sd","ratio.plus.sd",
                           "p.value.ratio","p.value.sample",
                           "log2.ratio","log2.variance")

CHANGES IN VERSION 1.1.3
------------------------
 - better matching of file patterns of peaklist and id in report
 - tab2xls improvements: 
   - fix when there are cells with preceeding colons - would think they are cell properties
   - fix row limitation of 65536 - add new worksheet with remaining lines
 - re-added ibspiked_set2 dataset as the xz requirement allows for additional data

CHANGES IN VERSION 1.1.2
------------------------

 - fixed handling of divergent identifications in one search engine
 - fixed number of spectra in isobar-analysis report
 - fixed recently introduced error when reading mgf file
 - identifications tab in XLS report is now in concise format
   - shared peptides are colored in gray
 - added xls report format = wide

CHANGES IN VERSION 1.1.1
------------------------

NEW FEATURES:

 - normalization can now be performed on individual channels (and channel pairs)
 - added semi-quantitative Quantitation with emPAI, dNSAF and spectral count
 - proteinInfo can now be gathered from Uniprot directly
 - added reporter intensity plot shpwing effect of normalization
 - added linear regression as ratio estimator
 - improved MA plot: added 'Infinity' on the axis

CHANGES IN VERSION 1.0.0
------------------------

 - first Bioconductor version (version bump to 1.0.0)!
 - slot name reporterMasses is renamed to reporterTagMasses
    to fix clash with method reporterMasses which fetches assayData(ibspectra)[["mass"]]
 - slot name reporterNames is renamed to reporterTagNames
    to distinguish from deprecated Biobase::reporterNames
 - added option 'scan.lines' to readIBSpectra: read mgf files in parts
    for large MGF files
 - use a function for protein reporting: create.reports.R
    properties.conf will be replaced by properties.R

CHANGES IN VERSION 0.2.5
------------------------

 - MSnbase support: Added functions to coerce from MSnSet to IBSpectra and vice versa.
   Added Msnbase to Suggests.
 - support for multiple classes added
 - updated Perl parsers: mascotParser2.pl and pidresParser2.pl instead of isobarXParser.pl
   resulting XML files can be converted to id.csv using psx2tab2.pl
 - prob otion for readIBSpectra worked errornous - fixed (thanks to Xavier Robin)
 - added property use.na: Use NA values for quantification
 - various Analysis Report beautifications (thanks to Xavier Robin)
 - varous bug fixes


CHANGES IN VERSION 0.2.4
------------------------

 - improved Vignette descriptions, added CITATION (still UTF-8 error)
 - added possibility to revert Mascot escaped TITLEs
 - if proteins are excluded w/ subsetIBSpectra, exclude all
   it's peptides, not only reporter-specific ones
 - fix error introduced in 0.2.3: When multiple MGFs were read,
   an false error occured that not all id spectra could be matched
 - add property 'author' for LaTeX reports
 - section 'Significantly regulated proteins' not shown anymore by default
   added property show.significant.proteins to reenable
 - added properties isotope.impurities and fragment.outlier.prob
 - bug fixes: 
   - naming not correct when class labels contain NAs
   - numeric class labels are not handled correctly
 - added naRegion to noise model
 - data is now stored before normalization. Those values are then used to normalize.
   (Thanks to observation of Chris Bielow)

CHANGES IN VERSION 0.2.3
------------------------

 - specify combination matrix for proteinRatios and in properties.conf
 - improved logging of IBSpectra creation and normalization
 - fix: maplot crashed on all NA channels
 - NA names in PDF report section 'Not quantified proteins' removed
 - allow for NA class labels - they are ignored in the comuptation of ratios

CHANGES IN VERSION 0.2.2
------------------------

 - re-added ratio vs intensity plot in QC report
 - issue warning when summarize property is incorrectly defined
 - create cachedir if it does not exist 
 - estimateRatio.group_specific_proteins renamed to quant.w.grouppeptides 
 - sanitize analysisname, uniprotlink, and subsection names for LaTeX
 - use fancyhdr instead of fanctheadings
 - added argument require.reporter.specific to reporterProteins


CHANGES IN VERSION 0.2.1
------------------------

 - Bug fix: as.data.frame generated ions/mass colnames with a 'X' in front


CHANGES IN VERSION 0.2
----------------------

 - Published online with JPR Publication
