# Interpreting aldex2 Results

**URL:** https://forum.qiime2.org/t/interpreting-aldex2-results/14996
**Category:** Library Support
**Created:** [May 18, 2020, 5:27pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996 "2020-05-18T17:27:37Z")
**Posts on this page:** 6
**Page:** 1

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### Author: ![vrbana](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/v/977dab/32.png) [@vrbana](https://forum.qiime2.org/u/vrbana)
#### Post date: [May 18, 2020, 5:27pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996/1 "2020-05-18T17:27:37Z")

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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:

```auto
qiime aldex2 extract-differences \
    --i-table gut-test/differentials.qza \
    --o-differentials gut-test/sig_gut \
    --p-sig-threshold 0.1 \
    --p-effect-threshold 0 \
    --p-difference-threshold 0

```

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](https://forum.qiime2.org/uploads/short-url/n6tMt1IF2eiODOWFWcSvUYGSou7.qza) (244.7 KB) [sig.qza](https://forum.qiime2.org/uploads/short-url/cAHIzKrhVHnKt1mBd4wrA2ODkK5.qza) (203.8 KB) [viz.qzv](https://forum.qiime2.org/uploads/short-url/u95vQhQKv6CtHk7fZfFURRpMqDr.qzv) (445.8 KB)

edit: tagging @dgiguer

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### Author: ![jbisanz](https://forum.qiime2.org/user_avatar/forum.qiime2.org/jbisanz/32/1720_2.png) [@jbisanz](https://forum.qiime2.org/u/jbisanz)
#### Post date: [May 18, 2020, 6:33pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996/2 "2020-05-18T18:33:35Z")

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It looks like it depends on if you use the t-test results (we.eBH) or the Wilcoxon/mann-whitney test (wi.eBH):

| Feature.ID | rab.all | rab.win.control | rab.win.vancomycin.1.day | diff.btw | diff.win | effect | overlap | we.ep | we.eBH | wi.ep | wi.eBH |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
| TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGTTAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTCGAGCCGTTGAAACTGGCAGACTTGAGTTGGCGAGAAGTACGCGGAATGCGCGGT | 1.324030 | -0.7753869 | 10.921798 | 11.41690 | 3.246717 | 3.318627 | 0.0002193 | 2.48e-05 | 0.0047024 | 0.000999 | 0.1667048 |
| TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGACTGTCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCCCGCCGTTGAAACTGGTGGTCTTGAGTGGATGAGAAGTACGCGGAATGCGTGGT | 0.328773 | -1.3907614 | 8.772128 | 10.32092 | 2.722074 | 3.909851 | 0.0002193 | 1.55e-05 | 0.0032193 | 0.000999 | 0.1667048 |

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### Author: ![dgiguer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/dgiguer/32/6140_2.png) [@dgiguer](https://forum.qiime2.org/u/dgiguer)
#### Post date: [May 19, 2020, 1:53pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996/3 "2020-05-19T13:53:38Z")

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> [@vrbana](#):
>
> I have to bump up the sig threshold to 0.45 to get the two features. Does this mean they are actually not significant?

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.

Cheers,

Dan

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### Author: ![vrbana](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/v/977dab/32.png) [@vrbana](https://forum.qiime2.org/u/vrbana)
#### Post date: [May 19, 2020, 4:01pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996/4 "2020-05-19T16:01:47Z")

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Hi Dan,

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

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### Author: ![dgiguer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/dgiguer/32/6140_2.png) [@dgiguer](https://forum.qiime2.org/u/dgiguer)
#### Post date: [May 22, 2020, 2:32pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996/5 "2020-05-22T14:32:50Z")

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Hi @vrbana,

You can find more information about what each of the outputs is [the ALDEx2 vignette](https://bioconductor.org/packages/release/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.pdf). You are correct in we.eBH is the BH-corrected values.

Dan

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 22, 2020, 8:40pm UTC](https://forum.qiime2.org/t/interpreting-aldex2-results/14996/6 "2020-06-22T20:40:21Z")

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