Changes in version 2.14.1 (2024-10-30) o Added interactive plotting functions using Plotly. o Integrated support for ProteinProspector data conversion via MSstatsConvert. Changes in version 2.6.1 (2023-02-26) o Minor change: update PhilosophertoMSstatsTMTFormat function normalization Changes in version 2.4.1 (2022-09-12) o Minor change: fix the bug of data table in performing local normalization Changes in version 2.2.7 (2022-02-18) o Minor change: extend PhilosophertoMSstatsTMTFormat function to have multiple types of input Changes in version 2.2.6 (2022-02-14) o Major change: add PhilosophertoMSstatsTMTFormat function as converter for outputs from Philosopher Changes in version 2.2.5 (2021-10-25) o Minor change: add different point shape to dataProcessPlotsTMT as indicator of imputed values Changes in version 2.2.3 (2021-10-06) o Minor change: fix the bug when df.prior is infinite Changes in version 2.2.0 (2021-09-21) o Major change: extend groupComparisonTMT() function to cover repeated measures design o Allow flexible order of condition in dataProcessPlotsTMT. o Fix bug in Condition label in dataProcessPlotsTMT. o Improve MSstatsTestSingleProteinTMT() by directly reading lmerTest output. This may make statistics slightly different due to different numeric accuracy o fix bug when condition name contains 'group' o change the x-axis order in profile plot Changes in version 2.0.1 (2021-06-14) o update comments of PD converter function o fix bug in proteinSummarization() function when MBimpute = F Changes in version 2.0.0 (2021-05-14) o Refactor the pacakge to make it modulized o parameter rmPSM_withMissing_withinRun was retired o change converter function output from data.frame to MSstatsValidated o change proteinSummarization() function output from data.frame to a list with two data.frames: FeatureLevelData and ProteinLevelData o change dataProcessPlotsTMT() function input from two data.frames to a list with two data.frames, which is the output of function proteinSummarization() o change groupComparisonTMT() function input from a data.frame to a list with two data.frames, which is the output of function proteinSummarization() o change groupComparisonTMT() function output from data.frame to a list with three items, ComparisonResult, FittedModel and ModelQC Changes in version 1.8.2 (2020-12-17) o Update progress bar o Update groupComparisonTMT to avoid reusing the local function copied from lmer pacakge Changes in version 1.8.1 (2020-12-10) o Add citation of the MSstatsTMT paper o Fix the bug in groupComparisonTMT() due to the update of dependent pacakge o Fix the bug in MedianPolish summarization o proteinSummarization(): replace the zero values with NA before and after peptide normalization Changes in version 1.6.6 (2020-10-13) o Fix the bug in converters due to fractions with same mean, sum and max values o Fix the bug in converters due to summaryforMultipleRows o Fix the bug in OpemMS converter due to duplicated rows Changes in version 1.6.3 (2020-06-05) o Allow NA in the annotation file Changes in version 1.6.2 (2020-06-02) o Fix the bug in proteinSummarization() function and make sure the input to dataProcess is data.frame Changes in version 1.6.1 (2020-05-10) o Update groupComparisonTMT() to make predictions for every protein Changes in version 1.4.7 (2020-04-24) o Update the NEWS file Changes in version 1.4.6 (2020-04-14) o Fix bug in groupComparison() for unbalanced design o Use df approximation from lmerTest to perform group comparison Changes in version 1.4.5 (2020-03-01) o Add new function OpenMStoMSstatsTMTFormat() Changes in version 1.4.4 (2020-02-01) o Fix bug in PDtoMSstatsTMTFormat(): remove redundant rows when combining multiple fractions Changes in version 1.4.3 (2019-12-28) o Fix bug in groupComparisonTMT(): very few measurements case previously doesn't work Changes in version 1.4.2 (2019-12-20) o Add the column 'issue' to the output of groupComparisonTMT() Changes in version 1.4.1 (2019-10-31) o Fix the bug in the PDtoMSstatsTMTFormat() due to different PD version Changes in version 1.2.7 (2019-08-22) o Update normalization options in proteinSummarization() function to include global protein normalization and local peptide normalization with respect to reference channel o Fix the bug in the contrast comparison of groupComparisonTMT() function. Changes in version 1.2.2 (2019-06-03) o Update the linear modeling in groupComparisonTMT() function. Implement 5 linear models. o Update the format of annotation file. If the channel has no sample, add 'Empty' under condition and BioReplicate columns. Changes in version 1.2.0 (2019-05-03) o Fix bugs in groupComparisonTMT() when using lm() function o Update the format of annotation file to include fraction column o Remove the 'fraction' option from coverter functions o Update the linear modeling in groupComparisonTMT() function Changes in version 1.0.0 (2018-09-21) o Submitted to Bioconductor