This workshop is a short introduction to dimension reduction methods, including Projection to Latent Structures Discriminant Analysis (PLS-DA) to analyse microbiome count data. We will cover the basic principles of data processing (from a table of count), to data exploration and identification of a microbial signature to discriminate different sample groups. We will use the R package mixOmics and one or two case studies (see also www.mixOmics.org for more details about the package and the workshops we run).
Key words: R, discriminant analysis, microbial signatures
Requirements: Software requirements: Install the latest version of mixOmics, as described here: http://mixomics.org/install/ on your laptop. Alternatively, you can sign for a free RStudio cloud account (https://rstudio.cloud/ ) and start the installation from there.
Assumed knowledge: A good working knowledge in R programming (e.g. handling data frame, perform simple calculations and display simple graphical outputs) is essential to fully benefit from the workshop. The course covers both theory and hands-on practice, with the opportunity to analyse your own data (if you have your data already processed as a table of counts!).
Relevance: The workshop will be relevant to those interested in analysing microbiome data, and in understanding the particular characteristics of those data.
Statistical Genomics, Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne
A/Prof Kim-Anh Lê Cao develops computational methods, software and tools to interpret big biological data and answer research questions efficiently. Kim-Anh has a mathematical engineering background and graduated with a PhD in statistics from the Université de Toulouse, France. She then moved to Australia to forge her own non-linear career path, first working as a biostatistician consultant at QFAB Bioinformatics, then as a research group leader at the biomedical University of Queensland Diamantina Institute.
She currently continues her strong research focus at the University of Melbourne. Kim-Anh has secured two consecutive NHMRC fellowships from 2014. In 2019 she received the Australian Academy of Science’s Moran Medal for her contributions to Applied Statistics. She was selected to the international HomewardBound leadership program for women in STEMM, culminating to a trip to Antarctica in 2019, and the superstars of STEM program from Science Technology Australia.