Wilcoxon RankSum Test
From MicrobeMS Wiki
Contents
Introduction
Wilcoxon ranksum test (Wikipedia)
To be continued
Parameter of the Wilcoxon ranksum test
 m/z range: boundaries of the m/z region in which the Wilcoxon ranksum tests are performed
 α: significance level of the Wilcoxon ranksum test
 dx (ppm): a parameter defining the width and the number of the m/z spectra segments. For example, a spectral segment centered at the position x covers a m/z interval of the width x * dx/10^6. The boundaries of the spectra segments are defined by [x*(1dx/(2*10^6))] and [x*(1+dx/(2*10^6))], respectively. For values of x = 2000 (m/z) and dx = 1000, the width of the respectice segment is 2 and the m/z values of the boundaries are 1999 and 2001.
 intensity: defines if barcode spectra or peak weighting factors are utilized as test inputs.
 show histogram: provides a histogram of the test outputs (pvalues, AUC, etc.) and gives also the mean, median and the standard deviation of the test variables.
Performing Wilcoxon ranksum tests
1. Load the mass spectral data files via the load spectra (Bruker data file format), import spectra from mzXML data, or the load MS multifile options of the File pulldown menu.
2. Wilcoxon ranksum tests are carried out from labeled spectra, i.e. from spectra with a class assignment. To perform the test label two groups of spectra as class 1 and as class 2, respectively. Labelling, or class assignment, can be carried out by selecting the appropriate spectra and choosing class assignments > class X from the Edit pulldown menu.
3. The test routine always starts from original MALDITOF mass spectra, i.e. spectral preprocessing and peak detection is carried out automatically using predefined parameters. Existing preprocessed spectra and predefined peak tables are ignored by the Wilcoxon ranksum tests.
4. Define test parameter, such as α (significance level), the m/z range and dx (ppm) which has a default value of 1000 (relative, in ppm). The parameter dx defines the width of m/z segments in which spectra are divided during the test. Peaks found in the same m/z segment are considered identical while mass peaks in different segments are considered different peaks.
5. When finished select peak frequency plots from the Analysis pulldown menu. Choose options from selection or from class X if the peak frequency test should involve selected spectra or spectra with an appropriate class labelling, respectively.
Output of Wilcoxon ranksum test
Example of the output from a series of Wilcoxon ranksum tests taken from the log file of MicrobeMS:
peakstats(tsttyp,prm,class) tsttyp: wilcx prm : 2 class : 0 ****************************************************** * univariate Wilcoxon rank sum tests * pvalues ****************************************************** number of spectra of class 1: 53 number of spectra of class 2: 55 start mass : 2000 m/z end mass : 12000 m/z alpha : 0.0001 allowed ppm : 1000 use peak intensities [0(NO)/1(YES)]: 0 #1, pvalues 1.9335e09 at m/z = 2518.0283 #2, pvalues 1.8206e08 at m/z = 8035.9213 #3, pvalues 1.0022e07 at m/z = 3876.8279 #4, pvalues 2.8756e07 at m/z = 6772.547 #5, pvalues 5.2462e07 at m/z = 6481.3235 #6, pvalues 4.5955e06 at m/z = 6552.5802 #7, pvalues 1.1652e05 at m/z = 3519.6031 #8, pvalues 1.1652e05 at m/z = 3983.3741 #9, pvalues 2.3408e05 at m/z = 2871.5769 #10, pvalues 0.00050564 at m/z = 3277.395 #11, pvalues 0.0023184 at m/z = 5033.1774 #12, pvalues 0.022862 at m/z = 2764.2031 #13, pvalues 0.036115 at m/z = 3178.2104 #14, pvalues 0.040747 at m/z = 3307.8312 #15, pvalues 0.04155 at m/z = 5525.5352 #16, pvalues 0.054108 at m/z = 4046.9202 #17, pvalues 0.073913 at m/z = 8090.9843 #18, pvalues 0.12303 at m/z = 6744.2579 #19, pvalues 0.15149 at m/z = 7059.8915 #20, pvalues 0.17526 at m/z = 2967.2566 #21, pvalues 0.1845 at m/z = 4591.731 #22, pvalues 0.20578 at m/z = 3352.5822 #23, pvalues 0.23769 at m/z = 5671.5438 #24, pvalues 0.30781 at m/z = 5438.3043 #25, pvalues 0.31723 at m/z = 6423.0388 #26, pvalues 0.31723 at m/z = 6844.4122 #27, pvalues 0.33142 at m/z = 7566.6528 #28, pvalues 0.3815 at m/z = 4815.43 #29, pvalues 0.43855 at m/z = 5953.9217 #30, pvalues 0.45125 at m/z = 4177.5814
