A script based on MetaboAnalystR (https://www.metaboanalyst.ca/home.xhtml) to analyse metabolomics data from targeted analysis of general metabolites. The objective is to present a condensed version with minimum necessary features, enabling the creation of standard plots (e.g. heatmap, correlation matrix, etc.). The script contains also a possibility to test for and remove outliers, based on Grubbs test and Outliers package (https://cran.r-project.org/web/packages/outliers/outliers.pdf).
A test dataset is included based on General Metabolite analysis of HT29 cells treated with 10 mM of Metformin and corresponding negative controls. Download of raw data (GenMet-Rdata.txt) via the "Code" button above.
For further practical details, including protocol for sample measurement, refer to Turtoi E et al. STAR Protocols 2023.
N.B.: Installation of specific R Packages (e.g. MetaboAnalystR & Outliers) is required before using the script; See the "Libraries" section of the script.