Changes in version 1.19.1 o Fix error in subsetIBSpectra and exclude and namespace imports (Laurent Gatto <2016-10-07 Fri>) Changes in version 1.17.1 o 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 o Bioconductor release 3.2 Changes in version 1.14.0 o Bioconductor release 3.1 Changes in version 1.13.0 o calcCumulativeProbXGreaterThanY() contributed by A. Stukalov, for calculating cummulative p-values with replicates o Bioconductor version increment Changes in version 1.12.0 o Bioconductor release 3.0 Changes in version 1.10.0 o Bioconductor release 2.9 Changes in version 1.9.5 o FIX FOR TMT-10plex tags: previous version had wrong annotation of N and C for 127,128,129,130 o Speed improvements for p-value calculation by vectorization, contributed by A. Stukalov Changes in version 1.9.3 o allow the use of a combination matrix in NoiseModel reporterTagNames o added function getProteinInfoFromTheInternet which automatically recognizes Uniprot and Entrez ACs. Set now as default 'protein.info.f' in the report configuration. o Overhauled isobar-analysis.Rnw o use of ltxtables to allow optimal column widths (longer runtime, however) o use [[ instead of $ for accession of lists o better column and grouping description o allow report generation without a proteinInfo object o set report cache directory to 'cache' (instead of '.') by default o 1.9.3.2: o mascotParser2.pl: allow to skip modif-conversion with -no-modiconv o mascotParser2.pl: set --lightXML as default o report generation: set combn.method="versus.channel", which computes the ratios against the first channel o various PDF report improvements o 1.9.3.3: o report tables are written into tables which are loaded with LTxtable report generation takes longer now o fixes in correct.peptide.ratios o use combined protein group for peptide-protein mapping o use only reporter proteins for mapping o fix in creation of protein groups from template, subset by peptide _and_ modif Changes in version 1.9.2 o fix issue of NA in 'n.spectra' when calculating summarized ratios o various report improvements: o use column of variable width to display class labels o add attributes of quant table to summarized result table o improved placement of tikz peptide group pictures Changes in version 1.7.6 o added TMT 10plex (contribution from Florent Gluck) o fixed bugs with system.file not working on R < 2.11 (contribution from Florent Gluck) o fixed bug in isobar-qc which was not working without normalize=TRUE o added writeHscoreData for usage with Hscorer.py (MM Savitski, 2010) o shQuote commands correctly - should fix issues running report generation on Windows o added calculations and XLS tab for peptides with unsure localization of the modification site o updated scripts for creating multi-sample reports (create.meta.reports) Changes in version 1.7.5 o fixed critical bugs: Excel report output had wrong ordering, ie ratios did not correspond to the meta information [introduced in version 1.7.3]. o fix of real peptide names: Reexport I/L peptides in reports Changes in version 1.7.4 o improved MSGF+ search result import o refactored report properties: all properties can now be defined in in the properties.R o speed and memory usage improvements when creating wide XLS report o ratio p-value adjustment now works per comparision instead of globally Changes in version 1.7.3 o fix wide XLS report format o novel plot for ratio combinations in QC report showing individual ratio distributions and significant ratios Changes in version 1.7.2 o added TMT 6plex masses to phosphoRS export script o fixed mascot parsers o MzIdentML version 1.1.0 support implemented [not fully tested] Changes in version 1.7.1 o fixed import of MzIdentML files from Mascot and ProteomeDiscoverer Changes in version 1.6.0 o added modules and functions for PTM quantification Changes in version 1.5.3 o 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 o added MSGF+ tsv import [one-line-per-psm format] o refactored various parts of the code (proteinRatios, report-utils, isobar-import) o PTM XLS report: report significance for protein ratio, and peptide ratio Changes in version 1.5.1 o added molecular weight correction to emPAI and dNSAF o added property 'ratiodistr.class.labels': biological variability can be calculated in the report with other labels o improved PDF analysis report: added number of proteins in each section o added location scale family T distribution as biological variability distribution (distr class) and fitTlsd. o better protein PDF analysis report layout. Changes in version 1.5 o Added modules for PTM validation and quantification o Validation o PhosphoRS XML import writers and outpout readers o DeltaScore calculation when the data is provided o Quantification o 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. o Correction of peptide ratios with protein ratios is possible. Also the variance can be adjusted (assuming no or full correlation) o Report generation o Import PhosphoSitePlus or neXtProt information on modification sites Changes in version 1.3.0 o Rockerbox import (just define the XXX.dat.peptides.csv as identifications) o 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 o better matching of file patterns of peaklist and id in report o tab2xls improvements: o fix when there are cells with preceeding colons - would think they are cell properties o fix row limitation of 65536 - add new worksheet with remaining lines o re-added ibspiked_set2 dataset as the xz requirement allows for additional data Changes in version 1.1.2 o fixed handling of divergent identifications in one search engine o fixed number of spectra in isobar-analysis report o fixed recently introduced error when reading mgf file o identifications tab in XLS report is now in concise format o shared peptides are colored in gray o added xls report format = wide Changes in version 1.1.1 NEW FEATURES o normalization can now be performed on individual channels (and channel pairs) o added semi-quantitative Quantitation with emPAI, dNSAF and spectral count o proteinInfo can now be gathered from Uniprot directly o added reporter intensity plot shpwing effect of normalization o added linear regression as ratio estimator o improved MA plot: added 'Infinity' on the axis Changes in version 1.0.0 o first Bioconductor version (version bump to 1.0.0)! o slot name reporterMasses is renamed to reporterTagMasses to fix clash with method reporterMasses which fetches assayData(ibspectra)[["mass"]] o slot name reporterNames is renamed to reporterTagNames to distinguish from deprecated Biobase::reporterNames o added option 'scan.lines' to readIBSpectra: read mgf files in parts for large MGF files o use a function for protein reporting: create.reports.R properties.conf will be replaced by properties.R Changes in version 0.2.5 o MSnbase support: Added functions to coerce from MSnSet to IBSpectra and vice versa. Added Msnbase to Suggests. o support for multiple classes added o updated Perl parsers: mascotParser2.pl and pidresParser2.pl instead of isobarXParser.pl resulting XML files can be converted to id.csv using psx2tab2.pl o prob otion for readIBSpectra worked errornous - fixed (thanks to Xavier Robin) o added property use.na: Use NA values for quantification o various Analysis Report beautifications (thanks to Xavier Robin) o varous bug fixes Changes in version 0.2.4 o improved Vignette descriptions, added CITATION (still UTF-8 error) o added possibility to revert Mascot escaped TITLEs o if proteins are excluded w/ subsetIBSpectra, exclude all it's peptides, not only reporter-specific ones o fix error introduced in 0.2.3: When multiple MGFs were read, an false error occured that not all id spectra could be matched o add property 'author' for LaTeX reports o section 'Significantly regulated proteins' not shown anymore by default added property show.significant.proteins to reenable o added properties isotope.impurities and fragment.outlier.prob o bug fixes: o naming not correct when class labels contain NAs o numeric class labels are not handled correctly o added naRegion to noise model o 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 o specify combination matrix for proteinRatios and in properties.conf o improved logging of IBSpectra creation and normalization o fix: maplot crashed on all NA channels o NA names in PDF report section 'Not quantified proteins' removed o allow for NA class labels - they are ignored in the comuptation of ratios Changes in version 0.2.2 o re-added ratio vs intensity plot in QC report o issue warning when summarize property is incorrectly defined o create cachedir if it does not exist o estimateRatio.group_specific_proteins renamed to quant.w.grouppeptides o sanitize analysisname, uniprotlink, and subsection names for LaTeX o use fancyhdr instead of fanctheadings o added argument require.reporter.specific to reporterProteins Changes in version 0.2.1 o Bug fix: as.data.frame generated ions/mass colnames with a 'X' in front Changes in version 0.2 o Published online with JPR Publication