Hello! I would like to report that I encountered 2 problems in the volcano plot tab in the Statistical Analysis module.
The first problem is that, at first glance, that the -log10(p) is not doing the calculation correctly. We discovered that what happens is that the calculation of the -log10(p) is not matching the line, in other words, the -log10(p) of one feature is showing in another line of another feature. Therefore the significant features displayed in the volcano plot are not correct - as the -log10(p) is being used to plot. Please note that I only see this problem when using a personal data, and not with the provided example data.
And secondly, I am unable to visualize the boxplots either by clicking on the volcano points or by clicking ‘view’, this happens even with the provided data available on MetaboAnalyst.
I look forward to hearing from you!
Best wishes,
Fernanda