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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
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
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This note was uploaded on 02/06/2014 for the course STAT 503 taught by Professor Staff during the Fall '08 term at Iowa State.
- Fall '08