Background Automated behavioural assessment is gaining a greater presence in the field of neurodegenerative disease research. It provides objectivity and a wide scope of uses in phenotyping but conversely presents difficulties due to the very advantages it presents: mainly, that the researcher is presented with a large amount of data which must be collated, prepared, explored and tested. Manual preparation of this data can also increase the risk of mistakes and thus decrease the reliability of results.
Aims In order to facilitate the exploration and analysis of data produced by the Labmaster and Phenomaster automated homecage system (TSE Systems), we undertook to create a system that would aggregate and process the raw data produced, present the results in an intuitive and visual manner to aid discovery and provide some additional tools to facilitate data analysis.
Methods The R Statistics software (R Development Core Team (2009)) was used to create a script to provide all the processing and analysis functions. For our analysis, we limited the variables analysed from the homecage output since not all are relevant or are coincide with the observations of other variables. Where inferential tests were applied, we used False Discovery Rate to adjust for multiple testing. The Manipulate package was used to give interactive functionality and the PLS package provided functions for partial least square regression.
Outcome The script we generated was able to produce the necessary aggregation and reduction of data from the csv files containing raw Labmaster/Phenomaster data, automatically adjusting for occasions when the metabolic attachment was present. The amount of time necessary to prepare, graph and export data was greatly reduced, while facilitating exploration of the data by use of multivariate analysis. We illustrate the outcomes from this analysis method with results from different rodent models of HD and HD-like diseases and experiments.
- Behaviour phenotype
- Huntington's disease
- automated homecage
- animal model
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