The number "n" appears to change depending on which way the comparison is run. Is there no guide that explain output for these visualizations?
Someone else asked the same question and no one ever answered them: "What does the value of N means and why does it oscillate between samples if the groups always consist of three replicas?"
Can anyone explain the plots please? What in the world is "n"?
Hello John,
Welcome to the forums. Let's dive right in.
What in the world is “n”?
It's the number of samples that have that level of a metadata factor. So
| Sample | Patient | Timepoint |
|---|---|---|
| 1 | A | 1 |
| 2 | A | 2 |
| 3 | A | 3 |
| 4 | A | 4 |
| 5 | A | 5 |
| 6 | B | 1 |
| 7 | B | 2 |
| 8 | B | 3 |
| 9 | B | 4 |
| 0 | B | 5 |
Patient A (n=5)
Parient B (n=5)
Timepoint 1 (n=2)
Timepoint 2 (n=2)...
Nope. But it is covered in this section of the primary tutorial 
https://docs.qiime2.org/2019.7/tutorials/moving-pictures/#alpha-and-beta-diversity-analysis
Let me know if you have any questions! We are all volunteers here, but we do our best to help.
Colin
That thread did not stay on topic, and was a bit of a mess, these things happen.
Please see this post for more info: How to interpret beta-group-significance results (boxplots)
Ah, thank you! I looked around but had not seen that post you linked to.
One more question about beta group significance boxplots: in the attached screenshot are the results of comparing male and female gut microbiomes from the same geographic location. Can you explain why I am getting two separate boxplots? I can’t wrap my head around why there is a “Distances to M” (male) boxplot that looks different from “Distances to F” (female). My flawed intuition would be that there is only one possible comparison here, male versus female, no?
There are three distances here:
The F-F & M-M are showing you the within-group pairwise distances, basically all the distances for the F (or M) samples. Make sense?
Yes! Excellent, thank you!
One more question about the n value that is the number of comparisons.
I have 19 males and 21 females. It makes sense that the M-F/F-M comparison has n=399 (1921). What I don’t understand is why M-M has n=171 (199??) and F-F has n=210 (21*10??). Any ideas?
Thanks!
Hey @John_Blazier,
Check out this post which explains where those numbers come from (it’s the number of pairwise comparisons within a group which make up the distribution).
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