P value adonis test + ancombc

[M_F (Meriem)]

Hello,

I have two questions :

1. I would like to know how to display p value after performing Adonis test because only the following parameters were displayed

Df	SumsOfSqs	MeanSqs	F.Model	R2	Pr(>F)

I need P value to evaluate the impact of confounded variables on the study .

Any advice

2)I applied Analysis of Compositions of Microbiomes with Bias Correction (ANCOMBC), the output file (differential abundance bar plot, x axis LFC, y axis Feature ID) shows a truncated Feature ID in y axis. (please see the screenshot)

Please let me how to display the entire feature ID, if it’s possible to extend the image size.

Best

[SoilRotifer (Mike Robeson)]

Hi @M_F,

I think you should be able to simply run qiime metadata tabulate ... on the differentials output of ancombc via --m-input-file. That should list all the p-values. Otherwise, I think the values appear in the visualizer when you mouse over the plot.

From within qiime composition da-barplot you can set --p-label-limit 700, or whatever value needed... to see all of the taxonomy.

Sometimes, I do not like having the full taxonomy, so I often use the vega editor (through the visualization), to trim the taxonomy string so that it only shows order through genus, or which ever taxonomy I'd like.

[M_F (Meriem)]

Hi @SoilRotifer ,

Thanks for the reply.

Regarding Adonis test, i asked if it’s possible to generate p values, i used the following command line

| qiime diversity adonis
--i-distance-matrix core-metrics-results/unweighted_unifrac_distance_matrix.qza
--m-metadata-file metadata.tsv
--o-visualization core-metrics-results/unweighted_adonis.qzv

–p-formula

could you give more details about the command line i can use to generate p value ?

Best

[SoilRotifer (Mike Robeson)]

Oh gosh, sorry about that @M_F.

You'll find the p-values under the "Pr(>F)" column. That is, the probability of obtaining an F-statistic as large as or larger than observed.

-Mike