Hello,
XCMS online is really convenient, but if I want to process more than two groups, shall I load them up together,then leading the result to the simca-p for further comparison?
We are planning to include multi-class comparison in the next release.
In the meantime, there are two ways to work around for comparing e.g. A vs B and A vs. C
1. If you just want to pull out a few features: run A vs. B and A vs. C separately. Correct p-values (e.g. Bonferroni).
2. run A vs. (B + C). You might want to reduce the minfrac (Alignment) parameter for this, since you will have more samples per class now.
Export the result and calculate A vs B and A vs. C statistics using other software.