Metabolomics Analysis in AltAnalyze

Metabolomics experiments typically produce quantitative values associated with chemical identifiers (PubChem, KEGGcompound, HMDB, ChEBI, CAS). AltAnalyze supports import and analysis of metabolomics data assuming:

  • IDs correspond to one of the above chemical ID systems
  • Quantitative values are non-zero (ideally log2)

Input IDs do not have to correspond to one of the above, but will if annotations and enrichment analyses are desired in AltAnalyze. Supported analyses include:

  1. Differential metabolite expression statistics (e.g., moderated t-test)
  2. Metabolite annotation (e.g., name, KEGG, WikiPathways)
  3. Sample classification (LineageProfiler)
  4. Marker prediction (MarkerFinder)
  5. Quantile and batch-effects normalization
  6. Hierarchical clustering
  7. 2D and 3D PCA
  8. Basic sample QC visualization
  9. Pathway enrichment analysis and visualization

Data Import

To import data, simple select the Vendor/data-type as Other ID and the appropriate ID system under the menu Select platform. Proceed with the default or customized options.