I have managed to get Aldex2 working, and have generated the attached plot. I am super happy with it so far, but I am a little unsure of how to interpret the graph. For log2(Foldchange), which direction represents my two levels? I have two levels, MOR and VEH. Does it consider the levels alphabetically? Asking this another way: do positive fold changes represent increases in MOR vs. VEH or VEH vs. MOR?
Hi!
Yes, groups will be ordered alphabetically.
Check the order of your groups in the output file. Positive effect size means greater abundance in the second group and negative in the first one.
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differentials.tsv (14.7 KB)
I've uploaded my differentials output. If I understand correctly, because MOR is listed first in the output, positive effect sizes mean greater in VEH?
That's correct!
Negative stands for MOR and positive for VEH.
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