2.7 years ago by
The relevant section of the methods is "Identification of metabolic pathways with significant expression changes." and "Statistical significance of the observed metabolic pathway expression patterns.".
You need to calculate if a pathway in up or down regulated for each of sample (tumor, condition, strain,...).
You can calculate this with GSVA package to calculate the enrichment score of each pathway per sample plus limma to find if the pathway is differentially expressed in Bioconductor.
- Then calculate the fraction of samples that a pathway is significantly differently expressed both up and down-regulated, that is your n and m.
- With this information for each pathway you can draw this plot.