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