5 data analysis case study

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Information about 5 data analysis case study

Published on February 17, 2014

Author: dgrapov

Source: slideshare.net

Biology Chemistry Comparison of Leaf Metabolites Informatics Comparison of pumpkin and tomatillo leaf primary metabolites Goal: Carry out a statistical, HCA, PCA and O-/PLS-DA analyses comparing leaf primary metabolite profiles (Used DATA: Pumpkin and Tomatillo 1.csv) Cucurbita pepo Physalis philadelphica

Biology Chemistry Comparison of Leaf Metabolites Informatics Comparison of pumpkin and tomatillo leaf primary metabolites Steps: 1.Identify analysis strategy (hint: use HCA and PCA) 2.Conduct statistical comparison 3.Identify top multivariate discriminants

Data Exploration Biology Chemistry Comparison of Leaf Metabolites Informatics Steps: 1. Identify the effect of treatment on species differences • Use HCA • PCA Exercise: Can different treatments be analyzed together to identify species differences?

HCA clustering of samples Biology Chemistry Comparison of Leaf Metabolites Informatics

Biology Chemistry Comparison of Leaf Metabolites Informatics raw PCA: comparison of pretreatments Mean centered Auto scaled

Biology Chemistry Identify Analysis Strategy Informatics Comparison of Leaf Metabolites Analysis Options: If the treatment is a minor effect compared to species differences: • two-sample t-Test for Species If the treatment is a has a considerable effect compared to species differences: • two-way ANOVA for Species + treatment + interaction (species/treatment) If the treatment has a similar effect size to species differences: • Eliminate one treatment type from analysis and use t-Test Conclusions: • Both PCA and HCA analyses suggests the treatment effect is minor • Using 12 compared to 6 samples per group will increased study power

Comparison PLS-DA to O-PLS-DA Biology Chemistry Informatics O-PLS-DA is only useful over PLS-DA when the axis of separation between two groups spans >1 dimension Comparison of Leaf Metabolites PLS-DA O-PLS-DA

Biology Chemistry Comparison of Leaf Metabolites Informatics Validation of PLS-DA model for discrimination between pumpkin and tomatillo leaf metabolites Outstanding model performance, highly unlikely by random chance

Biology Chemistry Comparison of Leaf Metabolites Informatics Identification of top multivariate discriminants between pumpkin and tomatillo leaf primary metabolites Could also select from increasing and decreasing metabolites separately

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