The contol included only adipic acid and pimeric acid

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Unformatted text preview: troduction and Background 10 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. Eg metabolomics 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 range of retention times. Two unique metabolite mixtures (mix1 and mix2) represent different experimental conditions (e.g. control and treatment). Each mixture was created independently twice, mimicking biological replicates of each experimental condition Four metabolite mixtures (2 conditions X 2 replicates) were derivatized and analyzed using gas chromatography coupled to mass spectrometry (GC/MS) in two independent experiments as technical replicates, demonstrated in table 2. The chemicals, their concentration and presence...
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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.

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