Institute for Advanced Biosciences Keio University
MathDAMP Mathematica package for differential analysis of metabolite profiles
Home Overview Examples Downloads TriDAMP References Contact
MathDAMP > Examples > 01-MathDAMP-QuickStart

01-MathDAMP-QuickStart

This notebook demonstrates the differential analysis of two datasets acquired by capillary electrophoresis coupled to a quadrupole mass spectrometer (CE-QMS) operated in selected ion monitoring (SIM) mode. The datafiles are part of the MathDAMP package. A parallel density plot of the two normalized datasets is shown along with a density plot representing the absolute×relative difference. Overlaid electropherograms in the vicinities of the most significant differences from the absolute×relative result are plotted as well. For a more in-depth step-by-step description of the procedure, please refer to the 03-MathDAMP-TwoDatasets.nb notebook.
Please assign the path leading to the MathDAMP files to the MathDAMPPath variable.

MathDAMPPath = "/home/baran/math/ms/MathDAMP.1.0.0/" ;

<< (MathDAMPPath<>"MathDAMP.m")

{ctrl, smpl} = DAMPImportMS[MathDAMPPath<>"/data/"<>#] &/@{"control.ms", "sample.ms"} ;

{ppctrl, ppsmpl} = DAMPRemoveNoise[DAMPSubtractBaselines[#]] &/@{ctrl, smpl} ;

rslt = DAMPTwoDatasets[ppctrl, ppsmpl, NormalizeGroupOptions {InternalStandardᢃ ... ems_cation.csv"], MemberQ[ppctrl〚2〛, 1.Round[#〚1〛]] &]}}] ;

DAMPParallelPlot[NormalizedDatasets/.rslt] ;

DAMPDensityPlot[AbsoluteRelative/.rslt] ;

DAMPPlotCandidates[NormalizedDatasets/.rslt, AbsoluteRelative/.rslt, PlotCount12, Pl ... amOptions {AnnotationTable (AlignedAnnotationTables/.rslt) 〚1〛}] ;

MathDAMP version 1.0.0 loaded (2006/04/26)

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[Graphics:HTMLFiles/index_11.gif]

[Graphics:HTMLFiles/index_12.gif]

[Graphics:HTMLFiles/index_13.gif]

[Graphics:HTMLFiles/index_14.gif]

[Graphics:HTMLFiles/index_15.gif]

IS normalization coefficients : {1., 0.952858}

[Graphics:HTMLFiles/index_17.gif]

[Graphics:HTMLFiles/index_18.gif]

[Graphics:HTMLFiles/index_19.gif]

[Graphics:HTMLFiles/index_20.gif]

[Graphics:HTMLFiles/index_21.gif]

[Graphics:HTMLFiles/index_22.gif]

[Graphics:HTMLFiles/index_23.gif]

[Graphics:HTMLFiles/index_24.gif]

[Graphics:HTMLFiles/index_25.gif]

[Graphics:HTMLFiles/index_26.gif]

[Graphics:HTMLFiles/index_27.gif]

[Graphics:HTMLFiles/index_28.gif]

[Graphics:HTMLFiles/index_29.gif]

[Graphics:HTMLFiles/index_30.gif]