# Maaslin2 significant results

**URL:** <https://forum.biobakery.org/t/maaslin2-significant-results/3607>\
**Category:** MaAsLin\
**Created:** [May 18, 2022, 6:31pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607 "2022-05-18T18:31:27Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Alya](https://avatars.discourse-cdn.com/v4/letter/a/e47c2d/32.png) [@Alya](https://forum.biobakery.org/u/Alya)\
**Post date:** [May 18, 2022, 6:31pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/1 "2022-05-18T18:31:27Z")

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Hi,

I ran maaslin2 on some microbial relative abundance data but I am confused about the results. In the significant results table I only see the following taxa that are significantly associated with my variables of interest (control vs treated and pre vs post randomization).

 ![Screen Shot 2022-05-18 at 2.22.58 PM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/f/fc630c23891a35617b61f76ad8134741542eb776.png)

However, when I open the all results table there are two additional taxa that have p-values \<0.05 (highlighted in yellow) that are not in the significant results table. Can someone please explain this?

 ![Screen Shot 2022-05-18 at 2.27.06 PM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/8/87301c6edf939759c2af3e467ca1495ec1339277.png)

Thanks for the help in advance.

Alya

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**Author:** ![lalas25](https://avatars.discourse-cdn.com/v4/letter/l/d78d45/32.png) [@lalas25](https://forum.biobakery.org/u/lalas25)\
**Post date:** [May 18, 2022, 6:40pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/2 "2022-05-18T18:40:51Z")

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Hi! The default settings are for Qvalue less than 0.25; That explains your discrepancy between all and significant results

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**Author:** ![Alya](https://avatars.discourse-cdn.com/v4/letter/a/e47c2d/32.png) [@Alya](https://forum.biobakery.org/u/Alya)\
**Post date:** [May 19, 2022, 3:38pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/3 "2022-05-19T15:38:17Z")

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Thanks @lalas25! I also found one taxa with a p-value \>0.05 highlighted below. what is the default cut off for p-values?

 ![Screen Shot 2022-05-19 at 11.37.10 AM](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/6/6d01f1e298deb2e61cca6e0d61a7f2147bf0ebd5.png)

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**Author:** ![lalas25](https://avatars.discourse-cdn.com/v4/letter/l/d78d45/32.png) [@lalas25](https://forum.biobakery.org/u/lalas25)\
**Post date:** [May 19, 2022, 4:00pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/4 "2022-05-19T16:00:46Z")

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The q-value for maximum significance is the only editable parameter with the flag max\_significance. So if it is under 0.25 (by default) it will make the significant results list even if p value is greater than 0.05

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<div class="post-metadata">

**Author:** ![Alya](https://avatars.discourse-cdn.com/v4/letter/a/e47c2d/32.png) [@Alya](https://forum.biobakery.org/u/Alya)\
**Post date:** [May 19, 2022, 4:05pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/5 "2022-05-19T16:05:30Z")

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My understanding is the q-value is generated from p-values that are below 0.05 for BH FDR method. So I’m not sure I understand how/why it is included in the significant results list.

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**Author:** ![Alya](https://avatars.discourse-cdn.com/v4/letter/a/e47c2d/32.png) [@Alya](https://forum.biobakery.org/u/Alya)\
**Post date:** [May 19, 2022, 4:15pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/6 "2022-05-19T16:15:38Z")

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Nvm I realize that was a silly question now since the qvalue is generated for all features. Thanks for your help @lalas25!

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**Author:** ![Sarah\_Vogel](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sarah_vogel/32/2055_2.png) [@Sarah\_Vogel](https://forum.biobakery.org/u/Sarah_Vogel)\
**Post date:** [March 21, 2023, 7:30pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/7 "2023-03-21T19:30:40Z")

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I would like to follow up here, as I am having a similar situation with my data. I have several taxa that fall within the specified q-value range, but with p-values above a 0.05 threshold. In cases where the p-value is greater than 0.05 but the q-value is below the established threshold, which value makes the most sense to use to determine statistical significance of the findings?

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**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [March 22, 2023, 2:38pm UTC](https://forum.biobakery.org/t/maaslin2-significant-results/3607/8 "2023-03-22T14:38:57Z")

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If you want to assess if the relationship is real, a plot will give you more insight than any p/q value. There should be one among the Maaslin2 outputs, look at that first.

It’s important to adjust for multiple comparisons, but if I was reviewing a paper I would be skeptical of results that didn’t even meet the nominal significance threshold. So you should consider both values.