permdisp in tutorial

Hi everyone,
I was reading the Parkinson’s Mouse Tutorial and in on section I saw this command:
qiime diversity beta-group-significance
–i-distance-matrix core-metrics-results/weighted_unifrac_distance_matrix.qza
–m-metadata-file metadata.tsv
–m-metadata-column cage_id
–o-visualization core-metrics-results/unweighted-unifrac-cage-significance_disp.qzv
–p-method permdisp
as you can see we import the weighted unifrac and then our output is unweighted unifrac. Is there any reason for this? could you please help me to understand this change?
Also, could you please let me know why we should use weighted (or unweighted)?
Thank you

1 Like

Hi @mohsen_ej,

There likely is a typo. The method does not change the technique, but the file is mislabeled. If you check the provenance, you can see whether the metric going into the test was weighted or unweighted.

Best,
Justine

Thank you for your information. so, should I use it with weighted or unweighted? or both? I mean which one is correct?

1 Like

Hi @mohsen_ej,

It’s an example of one way to do the analysis. Tutorial wise, I would match whichever metric you plan to use for adonis. Personally, I tend to run permdisp on whatever is significantly different in my data to check the distributions. There’s nothing quite like discovering the answer to “is there a difference” is “yes, nothing looks like itsself”.

Best,
Justine

2 Likes

Thank you for your help.

1 Like