CHANGES IN VERSION 3.3.4 ------------------------- - fix the bug for featureSubset=‘highQuality’ with label-based experiment. CHANGES IN VERSION 3.3.3 ------------------------- - add new option, remove_proteins_with_interference=FALSE (default), in dataProcess. whether it allows to remove proteins if deem interfered or not. CHANGES IN VERSION 3.3.2 ------------------------- - ProteinName=TRUE in groupComparisonPlots shows only the name of significant proteins, adjusting location. ggrepel package is used. - change featureSubset option in ‘dataProcess’ for selecting high quality features. featureSubset=‘highQuality’ - Fix the bug for ‘fillIncompleteRows=TRUE’ for label-based experiments. - change ‘quantification’ function. use run summarization from dataProcess. If there are technical replicates, use median run summarization for each subject. CHANGES IN VERSION 3.3.1 ------------------------- - fix the bug for volcano plot in groupComparisonPlots, with logbase=2. - update all plots for ggplot2 - Change the default for ‘cutoffCensored’. Now the default is “minFeature”. - for imputing the censored peak intensities, remove the features which has only 1 measurement for survreg function. CHANGES IN VERSION 3.2.3 ------------------------- - bug for normalization=‘globanstandards’ in dataProcess. Even though wrong normalization options, data processing is kept going. Make the process stop if wrong input for normalization - fix the bug with nameStandards=‘protein name’. (only peptide names worked with 3.2.2.) CHANGES IN VERSION 3.0.12 ------------------------- - remove vignetter folder to remove install and build error in Bioconductor CHANGES IN VERSION 3.0.9 ------------------------- - dataProcess - add options for ‘cutoffCensored=“minFeatureNRun”’. - summaryMethods=“TMP” : output will have ‘more50missing’column. - remove50missing=FALSE option : remove runs which has more than 50% of missing measurement. It will be affected for TMP, with censored option. - MBimpute : impute censored by survival model (AFT) with cutoff censored value - featureSubset option : “all”,”top3”, “highQuality” - change the default. -groupComparisonPlots - heatmap, for logBase=10, fix the bug for setting breaks. CHANGES IN VERSION 3.0.8 ------------------------- - dataProcess : when censoredInt=“0”, intensity=0 works even though skylineReport=FALSE. - dataProcess, with censored=“0” or “NA” : fix the bug for certain run has completely missing. - cutoffCensored=“minRun” or “minFeature” : cutoff for each Run or each feature is little less (99%) than minimum abundance. -summaryMethod=“TMP”, censored works. censoredInt=NA or 0, and cutoffCensored=0, minFeature, minRun CHANGES IN VERSION 3.0.3 ------------------------- - dataProcess : new option, skylineReport. for skyline MSstats report, there is ‘Truncated’ column. If Truncated==True, remove them. and keep zero value for summaryMethod=“skyline”. - groupComparison : for skyline option, t.test, val.equal=TRUE, which is no adjustment for degree of freedom, just pooled variance. CHANGES IN VERSION 2.1.4 ------------------------- - Change the numbering of file name for plots. If the file names are already existing in the folder, automatically next number will be add at the end of file name. Therefore file name will not be overwritten, and we can keep all pdf files for plots. CHANGES IN VERSION 2.1.3 ------------------------- - fix the groupComparison for label-free experiments. - automatically generate progress report as .txt files - add progress message for groupComparison and dataProcessPlots function. CHANGES IN VERSION 2.1.1 ------------------------- - fix the bug in Condition plot : 1. for label-based : match reference and endogenous 2. for label-free : when there is one observation in each group, SD=NA. make it zero. - fix the bug in heatmap and comparison plots : remove NA result for plotting - fix the bug for label-free groupComparison : how to get subject_nested parameter in make.contrast.free for unequal number per group - fix the bug in group quantification : make.contrast.group.quantification fixed for subject_nested parameter CHANGES IN VERSION 1.99.1 ------------------------- - fixed several NOTES, added .Rbuildignore, compacted vignettes - TODO: check remaining 'no visible binding for global variable' NOTES - removed warn -1 - added validity check when returning MSnSet - used inherits/is. for class testing - TODO fix if conditions syntax CHANGES IN VERSION 1.99.0 ------------------------- o improve efficiency for computing groupComparison and quantification <2012-12-21> o add .rnw <2012-12-03> o update groupComparision for label-free time-course experiment with single Feature and with or without technical replicates <2013-04-08> o add option for saving QQ plot and Residual plot in order to checkin the normality assumption in groupComparison function. <2013-04-08> o use ggplot2 package for all plots. <2013-07-11> o fix bug for volcano plot : different color labeling <2013-07-12> o add power plot in sample size calculation plot <2013-07-12> o add 'interference=TRUE or FALSE' in sample size calculation <2013-07-15> o add 'legend.size=7'for size of feature name legends in dataProcessPlots <2013-07-23> o add 'text.angle=0'for angle of condition labeling in dataProcessPlots <2013-07-23> o fix bug for quantification : when there are missing values in endogenous intensities, but values in reference intensities. <2013-07-24> o fix bug for groupComparison : when there are missing values in endogenous intensities, but values in reference intensities, .make.constast.based or .free sub function were changed. <2013-07-25> o two function for transformation between required input for MSstats and MSnSet class <2013-09-04> o flexibility for visualization : save as pdf files or show in window with selected proteins or all proteins. <2013-09-04> o handle unequal variance for feature in groupComparison function with featureVar=TRUE <2013-09-04> o Add 'missing.action' for impute missing values in group comparison stage. <2013-09-20>