Adapted from a MetaboAnalystR GitHub post
In general, we discourage the usage of traditional statistical methods - they are not suitable for omics data analysis. Some considerations from our perspective:
- Computationally expensive - when applied to 1000s of features …
- Statistically no well defined for multiple testing adjustment for interactions, post-hoc analysis
- Interface design are very complex to support 3-way ANOVA (better do it offline by experienced statisticians)
We recommend using the linear modelling (limma) for flexible multi-factor analysis - available in the Statistical Analysis [metadata] module.