Instructor Notes

General

  • The lesson takes about 8 hours of teaching and exercises (see the front matter of each episode). It assumes that learners know TreeSummarizedExperiment, agglomeration, transformation, ordination and the basics of machine learning, for example from the microbiome lesson. Not every learner has taken that lesson, so do not refer to its examples or dataset; the recap callout in episode 1 lists what is assumed.
  • Episode 1 has no code. Use it to introduce multi-omics, why the microbiome is studied with other data types, and the three groups of methods (exploratory, unsupervised, supervised), which structure the rest of the lesson. The section on how the data is generated is background: spend about 10 minutes on it, and stress the three take-homes: one transformation per data type, matched samples, and batches mixed up with the groups.
  • Episode 2 introduces the study (HintikkaXO) and the MultiAssayExperiment. primary and colname of the sampleMap() are identical in HintikkaXO, so use the rat C1 example to show the concept.
  • The summary page (episode 6) wraps up the whole lesson and how to choose a method. Leave about 10 minutes for it.
  • The episodes build on each other through the mae object prepared in episode 2 and kept in the R session; nothing is saved to disk. If a learner restarts R or falls behind, they can catch up by running the code of episode 2 again (a few seconds).
  • The setup page installs the packages with explicit commands instead of a script, so that learners see where each package comes from (Bioconductor, CRAN or GitHub). Go through it briefly at the start if needed.
  • The lesson uses plotJointRPCA() from miaViz, which is in the Bioconductor release from 3.24 on. Learners need the current release.
  • Live-code every chunk. The chunks are kept short on purpose, and the lesson uses only package functions, no custom helper functions.

Before the workshop

  • MOFA2 needs Python. The first run_mofa() installs a Python environment through basilisk, which can take 10 minutes or more. The setup page asks learners to train a test model before the workshop. Check this at the start of the workshop, at the latest before episode 4.
  • multiomics and IntegratedLearner are installed from GitHub; check that they installed.

The story of the lesson

All episodes use the HintikkaXO data: 40 rats on a high-fat or low-fat diet, with or without the prebiotic XOS, with microbiota, metabolites and host biomarkers. Two threads connect the episodes.

The fat thread

  • Episode 2 (challenge 2): fat has a large effect on the microbiota (PCA) and on butyrate, acetate and propionate.
  • Episode 3: the Mantel test is significant over all rats but weaker within the high-fat rats. Use challenge 1 to discuss how a shared factor (the diet) creates associations between data types. The butyrate challenge makes the same point for a single pair of features.
  • Episode 4: joint RPCA roughly separates the fat groups, and MOFA factor 1, shared by all three data types, separates them perfectly.
  • Episode 5: every data type predicts fat with AUC near 1.

The XOS thread

  • XOS was the intervention of the study, but its effect is small. MOFA finds no XOS factor (episode 4, challenge 3), IntegratedLearner predicts it with cross-validated AUCs of only 0.5–0.6, and the DIABLO cross-validated error is about 50 % (episode 5). Use this to discuss that integration does not create a signal, and that cross-validation is essential.

Consistent features

  • Glucose, butyrate and nicotinate come up in MiRKAT, MOFA factor 1 and DIABLO. Episode 5, challenge 2, asks learners to notice this.

Episode-specific notes

  • Episode 3: within the diet groups, the butyrate association is very different (about 0 in the high-fat rats, about 0.4 in the low-fat rats). Use it to show that associations over all samples can hide or create links.
  • Episode 4: run_mofa() warns that factor 3 follows the per-sample average of the metabolites; discuss it as a possible technical factor. The left/right direction of the joint RPCA map is computed inline, because the sign of an ordination axis is arbitrary.
  • Episode 5: IntegratedLearner’s seed argument only fixes the folds; set.seed() is needed for reproducible random forests. When every data type predicts the fat perfectly, the stacking weights change strongly with the seed. In challenge 3, the first DIABLO component of the XOS model separates the fat groups.

Notes on the data

  • The data comes with mia (data("HintikkaXOData")), so nothing is downloaded.
  • The taxonomy has SILVA prefixes (D_5__ for genus). The lesson keeps them to avoid custom code; mention that they do not change the analysis.
  • Many genera are uncultured; mia makes their names unique with a number (D_5__uncultured_2).
  • The metabolites have 27 missing values (below the detection limit), which episode 2 replaces with 0. The biomarkers have 95 missing values, which are kept: MOFA handles them, and IntegratedLearner drops those biomarkers (na.rm = TRUE).
  • Joint RPCA and MOFA use rclr values with impute = FALSE, so that the methods fill in the zeros themselves. The default rclr of mia (and vegan) returns a low-rank reconstruction, which would make the microbiota look perfectly explained in MOFA.

Common problems

  • Harmless warnings.
    • Many multiomics functions and getWithColData() warn 'experiments' dropped and print harmonizing input.
    • upsetSamples() prints deprecation warnings from UpSetR.
    • correlate_factors_with_covariates() warns that it converts the covariates to numbers.
    • MOFA warns about correlated factors; with 40 samples this is common.
    • block.splsda() prints that the design matrix has changed.
  • IntegratedLearner cannot find the outcome. It reads the outcome and the sample IDs from the colData of each experiment. Run the three getWithColData() lines of episode 5 first.
  • Known package issues. getMantel(group.by = ) fails on a MultiAssayExperiment (multiomics), so the lesson subsets the samples instead. The IntegratedLearner ROC plot leaves an empty lower half when there is no validation set.
  • DIABLO perf() and the seed. Use the seed argument of perf(), not set.seed(): with some versions of mixOmics and BiocParallel, a second perf() call after set.seed() fails with invalid value of 'seed'.
  • IntegratedLearner prints “training data”. The AUCs in its summary are cross-validated, despite the label.

Introduction to multi-omics

MultiAssayExperiment and the study data

Exploratory methods

Unsupervised methods

Supervised methods

Summary