Preamble

If you are following our online course, the following vignette will be useful as a complementary learning tool. This vignette also covers the essential use cases of various methods in this package for the general mixOmcis user. The below methods will be covered:

  • (s)PCA,
  • PLS1 and PLS2,
  • (s)PLS-DA,
  • N-integration (multi-block sPLS-DA, aka. “DIABLO”), and
  • P-integration (multi-group sPLS-DA, aka “MINT”).

As outlined in 1.3, this is not an exhaustive list of all the methods found within mixOmics. More information can be found at our website and you can ask questions via our discourse forum.

**Different types of analyses with mixOmics** [@mixomics].The biological questions, the number of data sets to integrate, and the type of response variable, whether qualitative (classification), quantitative (regression), one (PLS1) or several (PLS) responses, all drive the choice of analytical method. All methods featured in this diagram include variable selection except rCCA. In N-integration, rCCA and PLS enable the integration of two quantitative data sets, whilst the block PLS methods (that derive from the methods from @Ten11) can integrate more than two data sets. In P-integration, our method MINT is based on multi-group PLS [@Esl14b].The following activities cover some of these methods.

Figure 0.1: Different types of analyses with mixOmics (Rohart, Gautier, Singh, and Le Cao 2017).The biological questions, the number of data sets to integrate, and the type of response variable, whether qualitative (classification), quantitative (regression), one (PLS1) or several (PLS) responses, all drive the choice of analytical method. All methods featured in this diagram include variable selection except rCCA. In N-integration, rCCA and PLS enable the integration of two quantitative data sets, whilst the block PLS methods (that derive from the methods from Tenenhaus and Tenenhaus (2011)) can integrate more than two data sets. In P-integration, our method MINT is based on multi-group PLS (Eslami et al. 2014).The following activities cover some of these methods.