proteomics

Proteomics Analysis in AltAnalyze

Proteomics experiments typically produce quantitative values associated with protein, peptide or gene identifiers. AltAnalyze supports import and analysis of proteomics data assuming:

• IDs correspond to any of the many supported input 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 protein expression statistics (e.g., moderated t-test)
2. Protein/gene annotation (e.g., name, Pathways, Ontologies)
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.