February | 2015 | Creative Data Solutions

Archive for February, 2015

Winter 2015 Statistical and Data Analysis Workshop for Metabolomics

I recently had the pleasure of teaching the Winter 2015 Data analysis for Metabolomics workshop in collaboration with the West Coast Metabolomics Center. This years course featured the newly updated DeviumWeb (v0.4) and MetaMapR (v1.4.0) software. You can check all of the new features for yourself (DeviumWeb, MetaMapR).

I’ve bundled all of the course material to make it easy for anyone to download and follow along. You can download everything from DataAnalysisWorkshop.

February 7, 2015 | Categories: Uncategorized | Leave a comment

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Data visualization Gallery

Scatterplot matrix for overview of correlations and regressions, displaying box plots for Iris data species, variable histograms, correlation statistics, stripcharts and best fit lines.

Metabolites are represented by circular “nodes” linked by “edges” with arrows designating the direction of the biosynthetic gradient (i.e. substrate to product). Some metabolites are linked by more than one enzymatic step. Node sizes represent magnitudes of differences in plasma metabolite geometric means (ΔGM). Arrow widths represent magnitudes of changes in product over substrate ratios (ΔP:S). Colors of node borders and arrows represent the significance and direction of changes relative to non-diabetics as per the figure legend. Differences are significant at p<0.05 by Mann-Whitney U test adjusted for FDR (q = 0.1).

Figure 1. The type 2 diabetes-associated lipidomic changes projected in context of their biological relationships in obese African-American women.

Spearman’s correlations were used to generate multi-dimensionally scaled parameter connectivity networks for variable intercorrelations. Networks were oriented with fasting glucose at the origin and SFA in the lower right quadrant. Colored ellipses represent the 95% probability locations of metabolite classes (Hoettlings T2, p<0.05). Nodes indicate clinical parameters (diamonds), <20-carbon fatty acid metabolites (circles) and ≥20-carbon fatty acid metabolites (triangles), with discriminant model variables and glucose enlarged. Significant correlations between species are designated by orange (positive) or blue (negative) connecting lines (p<0.05, non-diabetic; p<0.01, diabetic participants).

Horizontal scatter plots of the log transformed concentrations for each model variable are shown. The horizontal arrangement of metabolite scatter plots is scaled to their loading in the discriminant model. A given species importance in the classification increases with increasing displacement from the origin (broken line). The direction of the displacement, left or right, designates whether the species was decreased (left) or increased (right) in the diabetic relative to the non-diabetic patients. The overall model discrimination performance is presented as a scatter plot of subject model scores (inset).

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