Compare more taxa simultaneously using pairwise-difference

[jakobjung]

Hello, I am currently using the longitudinal package to analyse pairwise differences between 2 groups (different diet) at 2 time-points (start and after 12 months). The pairwise-differences function works well on specific taxa, like here:

Doing a pairwise-analysis of bacteroidetes

qiime longitudinal pairwise-differences
--m-metadata-file ../data/metadata.tsv
--m-metadata-file ../data/OTU_level2.tsv
--p-metric "k__Bacteria;p__Bacteroidetes"
--p-group-column diet
--p-state-column months
--p-state-1 0
--p-state-2 12
--p-individual-id-column Id.patient
--p-replicate-handling random
--o-visualization ../analysis/pairwise-tests/bateroidetes_pw.qzv

Now I want to know whether it is possible to do the same for more taxa (optimally all) at the same time and ideally get an output table which shows p-values and differences etc. for each taxon instead of a visual output.
If not, is it maybe possible in phyloseq or other environments?
Thanks in advance, Jakob

[Nicholas_Bokulich]

@jakobjung

Now I want to know whether it is possible to do the same for more taxa (optimally all) at the same time and ideally get an output table which shows p-values and differences etc

Not possible in QIIME 2. We do not make this more convenient because the Wilcoxon test used in that action is not really appropriate for compositional microbiome data (has a high false-positive error rate). Yes, I know, we accept feature tables in that plugin but that is in part because feature tables can contain any type of count data, not just compositional microbiome data.

Instead, use ANCOM. The ANCOM action currently in QIIME 2 does not allow paired testing, but you can use ANCOM or DESeq2 in R to performed paired tests.