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