DIABLO TCGA Case Study

The full data set for this example (also including methylation data and 4 breast cancer subtypes) can be downloaded here. The example below illustrates an analysis on a smaller data set that is stored in the mixOmics package.

The R script used for all the analysis in this case study is available here.

More information on Plots

For a more in depth explanation of how to use and interpret the plots seen, refer to the following pages:

• plotIndiv() – Sample Plot
• plotArrow() – Arrow Plot
• plotVar() – Correlation Circle Plot
• circosPlot() – Circos Plot
• network() – Relevance Network Graph
• plotLoadings() – Loading Plots
• cim() – Cluster Image Maps

References

1. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, Van De Rijn M, Jeffrey SS, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Sciences, 98(19):10869–10874, 2001.
2. Cancer Genome Atlas Network et al. Comprehensive molecular portraits of human breast tumours. Nature, 490(7418):61–70, 2012.
3. Gonzalez, I, Le Cao, K.A., Davis, M.J. and Dejean, S., 2012. Visualising associations between paired ‘omics’ data sets. BioData mining, 5(1)
4. Singh, A, Gautier, B, Shannon, CP, Vacher, M, Rohart, F, Tebutt, SJ. and Le Cao, KA, 2016. DIABLO-an integrative, multi-omics, multivariate method for multi-group classification. bioRxiv, p.067611.
5. Rohart F, Gautier B, Singh A, Lê Cao K-A (2017). mixOmics: an R package for ‘omics feature selection and multiple data integration.
6. Rohart F, Mason EA, Matigian N, Mosbergen R, Korn O, Chen T, Butcher S, Patel J, Atkinson K, Khosrotehrani K, Fisk NM, Lê Cao K-A&, Wells CA& (2016). A Molecular Classification of Human Mesenchymal Stromal Cells, PeerJ 4:e1845