The chemicals their concentration and presence in

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Unformatted text preview: in each mixture are listed in table 1. Among them, nine metabolites: 3-aminobutyrate, lysine, fructose, glucose, adipic acid, isocitric acid, pimeric acid, shikimic acid, erythritol, were common to both mixtures. Eight metabolites, 4-aminobutyrate. Glycine, Leucine, Trehalose, Citric acid, malic acid, arabitol, and mannitol are only in mixture 1, and glutamine, maltose, Sucrose, ribose, malonic acid, keto-isovaleric acid, quinic acid, and succinic acid are only in mixture 2. The contol included only adipic acid and pimeric acid. 10 1 1.1 Introduction and Background Purpose Chromatoplots is an in-development R package for the analysis of metabolomic data collected via gas chromatography mass spectrometry (GC-MS). The package is co-authored by Tengfei Yin and Michael Lawrence. This analysis attempts to validate the component-grouping step of the chromatoplots pipeline, by using exploratory data analysis (EDA) and clustering methods to identify the number of unique metabolites present in the total list of components. Since the raw data includes both replicates and samples that share a subset of common entities, we anticipate identifying one group for each unique metabolite, in which the number of leaves in that cluster is equal to the number of samples in which that metabolite is present. 1.2 Experimental Design This data was collected by Suh-yeon Choi using gas chromatography mass spectrometry (GC-MS) in the summer of 2009 to mimic a typical metabolomics experiment. It contains two samples which mimic two experimental units, such as wild type and treatment group, and a control. Each sample was prepared twice (experimental replicates) and two aliquots from each replicate was tested (technical replicates), for a total of 4 replicates for each sample. The control was not replicated. Samples contain an mixture of artificial metabolites, representing extracts from living organisms. Included are multiple metabolite classes (amino acids, sugars, sugar alcohols, and various organic acids) with wide r...
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