I'm able to run everything fine and get plots that indicate two features are significantly different (appear red in the volcano plots). However, when I do the next part of the tutorial to extract these features, it appears they are not significant. If I run:
I get the error: " You have selected a significance threshold that is lower than minimum Q score (-p--sig-threshold). Select a higher threshold."
I have to bump up the sig threshold to 0.45 to get the two features. Does this mean they are actually not significant? differentials.qza (244.7 KB) sig.qza (203.8 KB) viz.qzv (445.8 KB)
As @jbisanz mentioned, it depends on the t-test that you use. Determining whether there is a true biological differences requires some interpretation using the context of your dataset. You will have to think about the nuances of your dataset to decide whether there is truly a biological difference or not.
So it appears the plots highlight with the raw p-values then while the “extract differences” function is going off the “we.eBH” (I assume that is benjamini hochberg corrected p-vals?). Because neither of my BH corrected pvals (we.eBH) or the Wilcoxon/mann-whitney test (wi.eBH) are below 0.1…
I assume we would never want to use the raw pvalues in any case