Version Compatibility

Reference examples tested with: MultiAssayExperiment 1.36+, SummarizedExperiment 1.40+, sva 3.50+.

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Deep per-omic normalization (DESeq2 VST internals, methylation noob/BMIQ, proteomics VSN) is owned by the per-omic categories and pinned to their own tool versions; this skill calls the cross-omic container and batch tools, so MultiAssayExperiment and sva are the binding versions here.

Data Harmonization for Multi-Omics

"Get my omics onto a common footing for integration" -> Transform each block to a comparable scale, equalize block contribution, decide a single batch strategy, and triage missingness - because the integrator sees one stacked matrix of numbers and spends its first factors on whichever block has the largest raw variance, which is a property of the assay, not the biology.

• R: MultiAssayExperiment to coordinate assays, sample map, and colData

Scope: cross-omic harmonization of already-normalized blocks - container assembly, transform choice, per-view scaling, batch strategy, missing-data triage. Deep single-omic normalization -> differential-expression, methylation-analysis, proteomics, metabolomics. The method-selection decision -> integration-design. Fusion math -> mofa-integration, mixomics-analysis. Single-omic RNA batch mechanics -> differential-expression/batch-correction.