CHANGES IN VERSION 1.3.1
------------------------

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
