… my data include samples collected from the same individual over different time points. When looking at the MetaboAnalyst file examples I see that you indicate paired data using -1, 1, -2, 2, -3, 3 etc. So I can see how to use this for experimental designs in which you have a sample pre and post treatment, but how do you indicate paired data in which a sample was assessed at more than 2 time points (baseline, 1 week and 2 weeks for example?)
Both MetaboAnalyst and MicrobiomeAnalyst accept a metadata table to describe complex study design. In this case, an example is given below (note time points can be more than two). You can use “Linear Model with Covariate Adjustment” (MetaboAnalyst) or “Multi-factor Analysis” (MicrobiomeAnalyst) to perform data analysis. In addition to “formal” statistical analysis, you can use heatmap and PCA to visually detect patterns with regard to different metadata.
