Pairwise-comparing OTUs frequency

longitudinal

(Vitor Heidrich) #1

Hi everyone,
I am trying to pairwise-compare OTUs frequencies across different DNA extraction methods (paired samples). I want to do this comparison for every feature in my relative-frequency collapsed table at levels 2-7.
Then I tried this

qiime longitudinal pairwise-differences \
    --i-table 700703out_OTU_table_97_filtered_relfreq_l{7}.qza \
    --m-metadata-file 700703out_mapping_file_gram.txt \
    --p-metric featuretable \
    --p-state-column DNA_extraction \
    --p-group-column DNA_extraction \
    --p-state-1 B \
    --p-state-2 M \
    --p-individual-id-column patient \
    --p-no-parametric \
    --o-visualization $VARTIFACT 

And got

Plugin error from longitudinal:

  metric must be a valid metadata or feature table column.

Debug info has been saved to /tmp/qiime2-q2cli-err-8ubeg6l4.log

Initially I thought this would work because I was just mirroring the answer by @Nicholas_Bokulich here, but obviously I am not setting the right metric. Which metric should I use to get the taxa comparisons?

Thank you in advance!


(Nicholas Bokulich) #2

You need to use the name of an actual feature. So a taxon name, ASV feature ID, whatever the feature labels are in your feature table. This command only operates on a single metric (for the time being).

The command I wrote in that separate topic was just a fixed version of the command written by the asker. featuretable was the name of their metric, and was probably just a place-holder.

Good luck!


(Vitor Heidrich) #3

Very useful answer!
Thanks