# Question about q-value for alpha diversity
**URL:** https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372
**Category:** User Support
**Created:** [November 6, 2020, 8:29pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372 "2020-11-06T20:29:37Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@saatkinson](https://forum.qiime2.org/u/saatkinson)
#### Post date: [November 6, 2020, 8:29pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/1 "2020-11-06T20:29:37Z")
Hello,
I am working to interpret the q-values for alpha group significance tests. I found [this post](https://forum.qiime2.org/t/kruskal-wallis-test-of-alpha-diversity/2211/9) that explains that the test is Benjamini Hochberg, but I'm unclear what the chosen FDR is to calculate the critical value. The [SciPy page](https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html) for multiple testing says "e.g. 0.1". Is this the default and was it used in Q2?
Additionally (from my understanding of BH) you find the largest p-value smaller than the critical value (while sorted) and anything above it (i.e. smaller) is considered significant. Should I be resorting the resulting pairwise tables on p-value (smallest to largest) and comparing the q-value to find which comparisons are significant? I've attached an output from observed features calculation to try an explain what I'm referring to.
[obs\_feat\_kruskal-wallis-pairwise-Cohort.csv](https://forum.qiime2.org/uploads/short-url/5mJwl3895pkwd1rfog4mLbh0cZ3.csv) (1.7 KB)
Thanks,
Samantha
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [November 10, 2020, 8:25am UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/3 "2020-11-10T08:25:03Z")
Hi @saatkinson,
QIIME 2 using the [statsmodels](https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html) multicompare under the hood which by default sets their p-value to 0.05. However, I'm not sure how many people rely on that sorted critical value; the underlying code simply pulls out the adjusted p-values and ignores the automatically calculated threshold.
My personal inclination is to be somewhat conservative if the univariate test is your final alpha diversity test; I tend to be a bit more permissive when I'm using it for metadata selection to feed into an adjusted model.
So, I'm not sure if the sorting will buy you anything personally, I guess it depends on how you want to work with the data and how you plan to go forward.
Best,
Justine
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### Author:  [@saatkinson](https://forum.qiime2.org/u/saatkinson)
#### Post date: [November 10, 2020, 5:43pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/5 "2020-11-10T17:43:22Z")
Hi @jwdebelius,
Thank you for your response! I'm still a little confused; sorry if this is super simple and I'm spacing. The group significance test is generally my final alpha diversity test. Therefore, do I need to be comparing the adjusted p-value number to 0.05 to determine if the pairwise test is significant?
Thanks,
Samantha
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [November 11, 2020, 8:46am UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/6 "2020-11-11T08:46:58Z")
Hi @saatkinson,
You want to compare to your critical value. I tend to send mine apriori at 0.05 based on historical traditions and the fact that most people assume I'm going to set it there anyway.
I don't know what your right p-value is, but you would compare the pairwise adjusted number to whatever p-value you set. I will say you haven't done a ton of comparisons here, and you probably don't have a lot of samples, so maybe this should factor in?
Best,
Justine
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### Author:  [@saatkinson](https://forum.qiime2.org/u/saatkinson)
#### Post date: [November 11, 2020, 5:59pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/7 "2020-11-11T17:59:55Z")
Hi @jwdebelius,
Perfect, I had been comparing the q-value to 0.05 (my standard alpha value as well) before I started questioning myself.
I'm unsure how to control for sample size/number of comparisons in the test. Do you have recommendations? Or are you suggesting to make the alpha value more/less stringent than 0.05?
Thanks!
Samantha
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### Author:  [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [November 12, 2020, 2:09pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/8 "2020-11-12T14:09:26Z")
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [November 12, 2020, 2:19pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/9 "2020-11-12T14:19:56Z")
Hi @saatkinson,
I would go with 0.05 if that's what you were going to set aprioi anyway.
Best,
Justine
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### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [November 12, 2020, 2:19pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/10 "2020-11-12T14:19:59Z")
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [December 13, 2020, 8:20pm UTC](https://forum.qiime2.org/t/question-about-q-value-for-alpha-diversity/17372/11 "2020-12-13T20:20:04Z")
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