# Can pval be used to compare microbial differences between the two groups only?

**URL:** <https://forum.biobakery.org/t/can-pval-be-used-to-compare-microbial-differences-between-the-two-groups-only/8749>\
**Category:** MaAsLin\
**Created:** [January 30, 2026, 9:30am UTC](https://forum.biobakery.org/t/can-pval-be-used-to-compare-microbial-differences-between-the-two-groups-only/8749 "2026-01-30T09:30:40Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Haylee](https://avatars.discourse-cdn.com/v4/letter/h/71c47a/32.png) [@Haylee](https://forum.biobakery.org/u/Haylee)\
**Post date:** [January 30, 2026, 9:30am UTC](https://forum.biobakery.org/t/can-pval-be-used-to-compare-microbial-differences-between-the-two-groups-only/8749/1 "2026-01-30T09:30:40Z")

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Hi, I am using MaAsLin2 with R version 4.4.2.

I have only one fixed\_effect, and it 's divided into two groups in the metadata table file. When I run MaAsLin2, there are pval and qval in the result file of all\_results.tsv, and only the result with qval \< 0.25 will appear in significant\_results.tsv.

- `pval`: the nominal significance of this association.
- `qval`: the corrected significance is computed with `p.adjust` with the correction method (BH, etc.).

Since I have only two groups in my analysis, could I directly use the pval to assess microbial differences between the two groups instead of qval? My concern is that BH correction is typically applied for multiple comparisons, but here I am making only a single comparison.

I hope someone can enlighten me on this. Thank you!

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**Author:** ![himel.mallick](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/himel.mallick/32/1757_2.png) [@himel.mallick](https://forum.biobakery.org/u/himel.mallick)\
**Post date:** [January 30, 2026, 10:09am UTC](https://forum.biobakery.org/t/can-pval-be-used-to-compare-microbial-differences-between-the-two-groups-only/8749/2 "2026-01-30T10:09:20Z")

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Even with only one fixed effect and two groups, MaAsLin2 is **not** performing a single statistical test. It is performing **one test per feature** (taxon, pathway, metabolite, etc.), all for the same group contrast. The multiple testing issue arises from testing many features in parallel, not from the number of groups in the metadata.

The p-value is the nominal, feature-wise statistic, while the q-value corrects for multiple testing across all features. Using raw p-values would only be appropriate if a single, pre-specified feature were tested. In typical microbiome analyses, q-values remain the appropriate measure of significance, even with just two groups.

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**Author:** ![Haylee](https://avatars.discourse-cdn.com/v4/letter/h/71c47a/32.png) [@Haylee](https://forum.biobakery.org/u/Haylee)\
**Post date:** [January 30, 2026, 10:29am UTC](https://forum.biobakery.org/t/can-pval-be-used-to-compare-microbial-differences-between-the-two-groups-only/8749/3 "2026-01-30T10:29:06Z")

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Thank you for the detailed explanation — it was very helpful. I’d like to clarify one more point: in my case, I’m only comparing the abundance of taxon between the two groups. Would you still recommend using the qval to assess significance in this scenario?

Thank you for your time and patience. I look forward to your guidance.