# \#permanova **URL:** https://forum.qiime2.org/tag/permanova/88.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [PERMANOVA and DESeq2: Re-evaluating Covariates After Subsetting by Time Point](https://forum.qiime2.org/t/permanova-and-deseq2-re-evaluating-covariates-after-subsetting-by-time-point/33242)
**Author:** [@Naorem](https://forum.qiime2.org/u/Naorem)\ **Replies:** 1\ **Last updated:** [June 9, 2025, 6:19pm UTC](https://forum.qiime2.org/t/permanova-and-deseq2-re-evaluating-covariates-after-subsetting-by-time-point/33242 "2025-06-09T18:19:19Z")
I have approximately 200 samples with outcome labels (success or failure) and various covariates, collected across multiple time points. My analysis plan includes using PERMANOVA to identify significant covariates, follo… --- ## [Using output from QIIME2, I'm getting this error Error in model.frame.default(formula = dist\_matrix ~ metadata$biome, drop.unused.levels = TRUE) : variable lengths differ (found for 'metadata$biome')](https://forum.qiime2.org/t/using-output-from-qiime2-im-getting-this-error-error-in-model-frame-default-formula-dist-matrix-metadata-biome-drop-unused-levels-true-variable-lengths-differ-found-for-metadata-biome/32724)
**Author:** [@Micro\_verse39](https://forum.qiime2.org/u/Micro_verse39)\ **Replies:** 1\ **Last updated:** [March 11, 2025, 7:58pm UTC](https://forum.qiime2.org/t/using-output-from-qiime2-im-getting-this-error-error-in-model-frame-default-formula-dist-matrix-metadata-biome-drop-unused-levels-true-variable-lengths-differ-found-for-metadata-biome/32724 "2025-03-11T19:58:10Z")
Apologies if this is the wrong place. I have been getting this error when producing PERMANOVA from unifrac output both in QIIME2 and when trying to produce it with various packages in R. I know this is saying there is a… --- ## [significant Permanova but non significant Permdisp](https://forum.qiime2.org/t/significant-permanova-but-non-significant-permdisp/29197)
**Author:** [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)\ **Replies:** 2\ **Last updated:** [February 9, 2024, 11:26pm UTC](https://forum.qiime2.org/t/significant-permanova-but-non-significant-permdisp/29197 "2024-02-09T23:26:32Z")
Hi friends! I have a doubt in statistical analysis, what does mean if i did a Permanova test and i got a pvalue of 0.01253 but, i ran a Permdisp test and i got a pvalue of 0.07? That could suggest a significant variatio… --- ## [Difficulty interpreting the results of Permanova and Bray Curtis](https://forum.qiime2.org/t/difficulty-interpreting-the-results-of-permanova-and-bray-curtis/28395)
**Author:** [@Linda\_Abenaim](https://forum.qiime2.org/u/Linda_Abenaim)\ **Replies:** 5\ **Last updated:** [November 23, 2023, 3:36pm UTC](https://forum.qiime2.org/t/difficulty-interpreting-the-results-of-permanova-and-bray-curtis/28395 "2023-11-23T15:36:09Z")
Hi everyone :grinning: Is anyone available to help me interpret and understand my beta diversity results? particularly Permanova and Bray Curtis. I am analysing the gut microbiome of an insect species raised on a treat… --- ## [significative adonis test, but no significance in paired adonis test?](https://forum.qiime2.org/t/significative-adonis-test-but-no-significance-in-paired-adonis-test/27807)
**Author:** [@kevin\_SalOrt](https://forum.qiime2.org/u/kevin_SalOrt)\ **Replies:** 3\ **Last updated:** [October 2, 2023, 10:27pm UTC](https://forum.qiime2.org/t/significative-adonis-test-but-no-significance-in-paired-adonis-test/27807 "2023-10-02T22:27:06Z")
Hi! Im comparing microbiota from different insect species, and i did by Permanova (or adonis) and i got a pvalue less than 0.05 but when i try to check which of them are different i got a P-paired value greather than 0.… --- ## [PERMANOVA and beta diversity analyses nested](https://forum.qiime2.org/t/permanova-and-beta-diversity-analyses-nested/27484)
**Author:** [@Edoardo\_Scali](https://forum.qiime2.org/u/Edoardo_Scali)\ **Replies:** 1\ **Last updated:** [August 27, 2023, 6:41pm UTC](https://forum.qiime2.org/t/permanova-and-beta-diversity-analyses-nested/27484 "2023-08-27T18:41:15Z")
Hello everyone, I have a question regarding beta diversity analysis and PERMANOVA. In my experimental design, I have categories with subgroups. For example: vegetation, cluster, species, plant. What I would like to do … --- ## [can I run anosim for interactions (two factors)?](https://forum.qiime2.org/t/can-i-run-anosim-for-interactions-two-factors/27096)
**Author:** [@MarwaTawfik](https://forum.qiime2.org/u/MarwaTawfik)\ **Replies:** 5\ **Last updated:** [August 3, 2023, 1:28pm UTC](https://forum.qiime2.org/t/can-i-run-anosim-for-interactions-two-factors/27096 "2023-08-03T13:28:16Z")
Continuing the discussion from Adonis vs. Anosim vs. Permanova: I checked your advice regarding the interaction of two factors using permanova, I used ANOSIM in my analysis so could I just stick to it in the interaction… --- ## [Using PERMANOVA in R to compare unbalanced groups with small sample size](https://forum.qiime2.org/t/using-permanova-in-r-to-compare-unbalanced-groups-with-small-sample-size/26618)
**Author:** [@col\_ahe](https://forum.qiime2.org/u/col_ahe)\ **Replies:** 5\ **Last updated:** [May 27, 2023, 1:35am UTC](https://forum.qiime2.org/t/using-permanova-in-r-to-compare-unbalanced-groups-with-small-sample-size/26618 "2023-05-27T01:35:13Z")
Hello everyone! I have been trying to use the pairwiseAdonis tool in R to compare different groups in my QIIME2 output. I converted my filtered SV table file, tree file, taxonomy file, and metadata file from QIIME2 into… --- ## [PERMANOVA analysis interpretation](https://forum.qiime2.org/t/permanova-analysis-interpretation/25862)
**Author:** [@malenaamer](https://forum.qiime2.org/u/malenaamer)\ **Replies:** 2\ **Last updated:** [March 28, 2023, 4:40am UTC](https://forum.qiime2.org/t/permanova-analysis-interpretation/25862 "2023-03-28T04:40:20Z")
Hi everyone, Could you help me interpret why are the p-values from my PERMANOVA overall results different from the pairwise results if the test statistic is the same? !qiime diversity beta-group-significance --i-di… --- ## [Does the skbio PERMANOVA function have a pairwise option like in qiime2?](https://forum.qiime2.org/t/does-the-skbio-permanova-function-have-a-pairwise-option-like-in-qiime2/25497)
**Author:** [@Sam\_Degregori](https://forum.qiime2.org/u/Sam_Degregori)\ **Replies:** 2\ **Last updated:** [February 14, 2023, 6:33pm UTC](https://forum.qiime2.org/t/does-the-skbio-permanova-function-have-a-pairwise-option-like-in-qiime2/25497 "2023-02-14T18:33:01Z")
Hi all, I know how to run the basic skbio permanova code in python: import skbio as skb skperm=skb.stats.distance.permanova(dm, host\_md\_test, column='Host1', permutations=999) But I only get stats on the overall te… --- ## [PERMANOVA analysis in Jupyter notebook](https://forum.qiime2.org/t/permanova-analysis-in-jupyter-notebook/25395)
**Author:** [@malenaamer](https://forum.qiime2.org/u/malenaamer)\ **Replies:** 3\ **Last updated:** [February 6, 2023, 10:41pm UTC](https://forum.qiime2.org/t/permanova-analysis-in-jupyter-notebook/25395 "2023-02-06T22:41:33Z")
Hello, I'm new to programing but Jupyter notebook is helping me keep track. Is there a way to obtain the beta diversity PERMANOVA results different from the .qzv file using Python? I tried using: from skbio.stats.dis… --- ## [how to take into account sample replicates in beta-group-significance testing?](https://forum.qiime2.org/t/how-to-take-into-account-sample-replicates-in-beta-group-significance-testing/25208)
**Author:** [@Dot](https://forum.qiime2.org/u/Dot)\ **Replies:** 4\ **Last updated:** [January 14, 2023, 6:30pm UTC](https://forum.qiime2.org/t/how-to-take-into-account-sample-replicates-in-beta-group-significance-testing/25208 "2023-01-14T18:30:22Z")
Hello, I was wondering if it's necessary to take into account repeated measures or nested relationships when performing beta diversity significance testing, such as with beta-group-significance or adonis? If so, is it p… --- ## [PERMANOVA on small sample size?](https://forum.qiime2.org/t/permanova-on-small-sample-size/23913)
**Author:** [@MarwaTawfik](https://forum.qiime2.org/u/MarwaTawfik)\ **Replies:** 1\ **Last updated:** [August 16, 2022, 9:02pm UTC](https://forum.qiime2.org/t/permanova-on-small-sample-size/23913 "2022-08-16T21:02:06Z")
Hi team, Could you please let me know what are the lowest sample size that could be considered acceptable? I did the ordination plot and can see the difference/dissimilarity visually between intestine, feed, and water. … --- ## [Does it make sense to explore differential abundant OTUs, when 2 groups are not significantly differente according to Permanova?](https://forum.qiime2.org/t/does-it-make-sense-to-explore-differential-abundant-otus-when-2-groups-are-not-significantly-differente-according-to-permanova/20804)
**Author:** [@smd](https://forum.qiime2.org/u/smd)\ **Replies:** 5\ **Last updated:** [September 24, 2021, 8:15pm UTC](https://forum.qiime2.org/t/does-it-make-sense-to-explore-differential-abundant-otus-when-2-groups-are-not-significantly-differente-according-to-permanova/20804 "2021-09-24T20:15:14Z")
Hello community, For the past few days, in my Lab, we have been struggling with the following question: Does it make sense to explore differential OTUs (form ASVs to phyla) in two groups that are not significantly diffe… --- ## [What was the model used for the PERMANOVA (e.g. free permutations of residuals - n=5 does not allow for many permutations at the lowest level)?](https://forum.qiime2.org/t/what-was-the-model-used-for-the-permanova-e-g-free-permutations-of-residuals-n-5-does-not-allow-for-many-permutations-at-the-lowest-level/20414)
**Author:** [@YuZhang](https://forum.qiime2.org/u/YuZhang)\ **Replies:** 3\ **Last updated:** [August 10, 2021, 3:38pm UTC](https://forum.qiime2.org/t/what-was-the-model-used-for-the-permanova-e-g-free-permutations-of-residuals-n-5-does-not-allow-for-many-permutations-at-the-lowest-level/20414 "2021-08-10T15:38:59Z")
Dear all， I used qiime2 to get a pcoa file of Bray-Curtis dissimilarity matrix and the significant difference from PERMANOVA . But when asked "What was the model used for the PERMANOVA (e.g. free permutations of residua… --- ## [Unbalanced sampling design and permanova](https://forum.qiime2.org/t/unbalanced-sampling-design-and-permanova/20179)
**Author:** [@Eman](https://forum.qiime2.org/u/Eman)\ **Replies:** 3\ **Last updated:** [August 7, 2021, 2:11pm UTC](https://forum.qiime2.org/t/unbalanced-sampling-design-and-permanova/20179 "2021-08-07T14:11:31Z")
Hello, I have the same issue. My project includes samples from different plant genotypes, but the reads generated from the wildtypes are very low leading to being excluded from the analysis while choosing a good samplin… --- ## [Error in Beta Diversity - Pairwise sampling](https://forum.qiime2.org/t/error-in-beta-diversity-pairwise-sampling/7895)
**Author:** [@BeckyNesnevich](https://forum.qiime2.org/u/BeckyNesnevich)\ **Replies:** 1\ **Last updated:** [January 21, 2019, 9:24am UTC](https://forum.qiime2.org/t/error-in-beta-diversity-pairwise-sampling/7895 "2019-01-21T09:24:07Z")
Hello, I have been trying to run the beta-group-significance command using the option "--m-metadata-column Description" and have been getting this error message: "All values in the grouping vector are unique. This meth… --- ## [Permanova analysis for distances](https://forum.qiime2.org/t/permanova-analysis-for-distances/18649)
**Author:** [@timanix](https://forum.qiime2.org/u/timanix)\ **Replies:** 7\ **Last updated:** [February 26, 2021, 7:25pm UTC](https://forum.qiime2.org/t/permanova-analysis-for-distances/18649 "2021-02-26T19:25:40Z")
Dear Qiimers! I have a question about permanova analysis. Permanova may be used both to test multiple groups together and in the pairwise mode. So, if I want to perform a post hoc analysis after permanova, is it an ap… --- ## [How to properly design formulas in Adonis ?](https://forum.qiime2.org/t/how-to-properly-design-formulas-in-adonis/17996)
**Author:** [@Erwan](https://forum.qiime2.org/u/Erwan)\ **Replies:** 3\ **Last updated:** [January 12, 2021, 2:44pm UTC](https://forum.qiime2.org/t/how-to-properly-design-formulas-in-adonis/17996 "2021-01-12T14:44:06Z")
Dear Qiime community, After spending hours reading about it, and lacking of knowledge about GLM, I am still struggling about the proper way to design model formulas to run Adonis. Especially, I'm facing two questions : … --- ## [Plugin error from diversity QIIME 2020.8 PERMANOVA](https://forum.qiime2.org/t/plugin-error-from-diversity-qiime-2020-8-permanova/17092)
**Author:** [@Hasinika](https://forum.qiime2.org/u/Hasinika)\ **Replies:** 1\ **Last updated:** [October 15, 2020, 8:36am UTC](https://forum.qiime2.org/t/plugin-error-from-diversity-qiime-2020-8-permanova/17092 "2020-10-15T08:36:35Z")
Hi, I am trying to conduct PERMANOVA on QIMME 2 2020.8 using the following command; $ qiime diversity beta-group-significance --i-distance-matrix core-metrics-results\_11995/unweighted\_unifrac\_distance\_matrix.qza --m… --- ## [comparing dissimilarity within and between groups (adonis-anosim-Kendall's W)](https://forum.qiime2.org/t/comparing-dissimilarity-within-and-between-groups-adonis-anosim-kendalls-w/15121)
**Author:** [@Cravo\_Adri](https://forum.qiime2.org/u/Cravo_Adri)\ **Replies:** 0\ **Last updated:** [May 27, 2020, 1:49pm UTC](https://forum.qiime2.org/t/comparing-dissimilarity-within-and-between-groups-adonis-anosim-kendalls-w/15121 "2020-05-27T13:49:24Z")
Hi, everyone, I have a general question about dissimilarity within-between groups, to which I could not find a conclusive answer so far. Broadly speaking, I have 5 samples per lake per time point (3 time points per yea… --- ## [PERMANOVA- beta-group-significance](https://forum.qiime2.org/t/permanova-beta-group-significance/15019)
**Author:** [@idapantoja](https://forum.qiime2.org/u/idapantoja)\ **Replies:** 3\ **Last updated:** [May 20, 2020, 5:28am UTC](https://forum.qiime2.org/t/permanova-beta-group-significance/15019 "2020-05-20T05:28:32Z")
Hi all, Hope everyone is doing well. I have a question specifically for the step calculating the PERMANOVA using the command beta-group-significance. Is there a way I can calculate the R2 there and get the value in t… --- ## [Understanding PERMANOVA QIIME2 Statistics for Beta Diversity](https://forum.qiime2.org/t/understanding-permanova-qiime2-statistics-for-beta-diversity/14048)
**Author:** [@LVC](https://forum.qiime2.org/u/LVC)\ **Replies:** 4\ **Last updated:** [March 16, 2020, 2:44pm UTC](https://forum.qiime2.org/t/understanding-permanova-qiime2-statistics-for-beta-diversity/14048 "2020-03-16T14:44:05Z")
Hello, I have had a look through the forum and these pages but I am still a bit confused so would appreciate some clarification on the PERMANOVA statistics. I have run the following command: beta-group-significance: … --- ## [Determining dispersion for beta diversity](https://forum.qiime2.org/t/determining-dispersion-for-beta-diversity/12747)
**Author:** [@Andrew\_Richards](https://forum.qiime2.org/u/Andrew_Richards)\ **Replies:** 2\ **Last updated:** [December 5, 2019, 8:14pm UTC](https://forum.qiime2.org/t/determining-dispersion-for-beta-diversity/12747 "2019-12-05T20:14:21Z")
Hey all, I have read quite a few other posts on this but I am not sure I understand the solutions fully. To sum up my experiment, I have conditioned soil with different cover crop treatments for 3 months and I want to … --- ## [PCoA and PERMANOVA results seem to contradict each other for beta diversity analysis](https://forum.qiime2.org/t/pcoa-and-permanova-results-seem-to-contradict-each-other-for-beta-diversity-analysis/11065)
**Author:** [@NC\_Cavan](https://forum.qiime2.org/u/NC_Cavan)\ **Replies:** 3\ **Last updated:** [August 13, 2019, 10:14pm UTC](https://forum.qiime2.org/t/pcoa-and-permanova-results-seem-to-contradict-each-other-for-beta-diversity-analysis/11065 "2019-08-13T22:14:59Z")
Hello, I am having a difficult time understanding what the output files from some of my beta diversity analyses mean (I am using QIIME2 version 2018.6). My metadata includes a categorical variable with two levels: “Yes”… --- ## [ADONIS: correct interpretation of interaction among factors](https://forum.qiime2.org/t/adonis-correct-interpretation-of-interaction-among-factors/10327)
**Author:** [@ja.morillo](https://forum.qiime2.org/u/ja.morillo)\ **Replies:** 1\ **Last updated:** [June 21, 2019, 11:04am UTC](https://forum.qiime2.org/t/adonis-correct-interpretation-of-interaction-among-factors/10327 "2019-06-21T11:04:24Z")
Dear Qiime2 Experts: This is a question related to the interpretation of the output of the plugin "qiime diversity adonis", that I am starting to use. We have rRNA 16S V4 data from a simple experimental design. In a soi… --- ## [Adding more functions to PERMANOVA](https://forum.qiime2.org/t/adding-more-functions-to-permanova/4729)
**Author:** [@yanxianl](https://forum.qiime2.org/u/yanxianl)\ **Replies:** 5\ **Last updated:** [March 11, 2019, 9:04pm UTC](https://forum.qiime2.org/t/adding-more-functions-to-permanova/4729 "2019-03-11T21:04:01Z")
Hi, In QIIME2, PERMANOVA is used to evaluate whether between-group distances are larger than within-group distance. Based on what I read in the GUSTA ME website, I have the following suggestions to extend PERMANOVA func… --- ## [PCO trajectory to mean of replicates](https://forum.qiime2.org/t/pco-trajectory-to-mean-of-replicates/7322)
**Author:** [@arwqiime](https://forum.qiime2.org/u/arwqiime)\ **Replies:** 2\ **Last updated:** [December 7, 2018, 2:03pm UTC](https://forum.qiime2.org/t/pco-trajectory-to-mean-of-replicates/7322 "2018-12-07T14:03:21Z")
Hello, I have analysed 16S data of cultures that were inoculated from an environmental community (0d=start) in 5 separate cultures and followed over a period of 50 days (17d, 32d, and 50d). Amplicon sequencing was done … --- ## [Beta diversity significance values not as expected](https://forum.qiime2.org/t/beta-diversity-significance-values-not-as-expected/7317)
**Author:** [@Masha\_T](https://forum.qiime2.org/u/Masha_T)\ **Replies:** 1\ **Last updated:** [December 7, 2018, 10:16am UTC](https://forum.qiime2.org/t/beta-diversity-significance-values-not-as-expected/7317 "2018-12-07T10:16:29Z")
Hello, I am running beta group significance to see what days are significantly different from other days, and I'm surprised by my results. Based on the taxonomic bar plots of my samples from group 1 or group 2 (both ov… --- ## [Beta group significance. High p-value in Permanova testing](https://forum.qiime2.org/t/beta-group-significance-high-p-value-in-permanova-testing/6681)
**Author:** [@Jo\_mee](https://forum.qiime2.org/u/Jo_mee)\ **Replies:** 3\ **Last updated:** [November 2, 2018, 12:00am UTC](https://forum.qiime2.org/t/beta-group-significance-high-p-value-in-permanova-testing/6681 "2018-11-02T00:00:27Z")
Hi everyone, I am trying to analyze microbiome content and obtain taxonomic heatmap and weighted UniFrac PCoA plot. I am trying moving pictures tutorial and each day something clarifies to later confuse me in following … [Next page](https://forum.qiime2.org/tag/permanova/88.md?match_all_tags=true&page=1&tags%5B%5D=permanova)