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