Is it possible to stratify diversity analyses by multiple metadata columns?

(Tomas Eagan) #1

I am looking at various diversity metrics for three study categories (i.e “IPF”, “KTR”, “COPD”), after having performed qiime diversity core-metrics-phylogenetic.
For each of the three categories there are three sub-categories (“OW”, “BAL”, “RSB”), and I´d like to look at stratified analyses; that is for instance difference in Faiths PD alpha-diversity for “OW” between "IPF, “KTR” and “KOLS”. And then afterwards for “BAL” and so on.
However, I can not from the visualizer generated with qiime diversity alpha-group-significance categorize by more than one metadata column.
I tried making a metadata file excluding the “BAL” and “RSB” samples (thus containing 1/3 of the original metadata file), but this generated an error message related to missing samples.

There must be a (simple) way to perform analyses stratified by multiple metadata columns, sorry if this is a completely basic question.

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(Nicholas Bokulich) #2

Hi @Tomas,
qiime diversity adonis can perform multi-way PERMANOVA. For alpha diversity, there is nothing in the release version of QIIME 2 (there is an ANOVA action in a development branch of QIIME 2, so April’s release of QIIME 2 will most likely have this functionality). For now, you can use qiime metadata tabulate to merge your alpha diversity data with your metadata, download as csv, and read into R or other statistical software to accomplish this.

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(system) closed #3

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