CHANGES IN VERSION 1.2.1 ------------------------ - 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