How to explain and interpret the ANOVA analysis

Hi team,
Hope you are well and thank you for initiating the forum.
I would like to ask few questions regarding ANOVA:

  1. When using the FDR of 0.05 in ANOVA analysis, my understanding is that any feature lies above the cut-off indicating that the feature is significant at least one of the groups. On the one hand, some features seem to be appeared above the cut-off, yet they were insignificant shown as green. How did the green features pass the threshold?
  • For some reason, the figure did not show up after uploading here.
  1. Y axis corresponds to -log10(raw p value). If FDR cut-off is applied to data, does it mean Y axis will be corresponding to the adjusted p value, which is the FDR value?
  2. Few selected features shown in the boxplot were displayed in both negative to positive scale like 2 groups are in positive scale while 1 group is in negative scale. How does MetaboAnalyst calculate it?

ANOVA settings: 1) FDR cut-off:0.05, 2) post-hoc analysis: Fisher’s LSD
Thank you for the clarification and help.

  1. It is hard to see what you mean by “green” without a screenshot.

  2. Y-axis is the raw p-value, not the FDR adjusted p-value. Points are coloured if the FDR value is below the cut-off. You can click the table icon to see the raw and FDR p-values for all significant metabolites.

  3. The boxplots show the metabolite level values, both ‘original’ (left) and ‘normalized’ (right). There are many different normalization methods - please search other posts/read details on the normalization page to learn about the method you selected.

Thank you for the explanation.

Please see the image regarding the 1st question.

Thanks for the screenshot.

That line is the raw p-value = 0.05 (so, -log10(0.05) = ~1.3). We realize this is confusing because we do not actually use this threshold to determine significance. We’ve removed the line from the plot, and MetaboAnalyst will be updated shortly.

To summarize: red points = significant = adjusted p-value < 0.05. green = not significant = adj. p-val > 0.05.