Hi everyone!
I'm doing a 16s metagenomic analysis in Qiime2, and I have obtained surprising results from a ANCOM analysis, which I could't explain: My feature-table includes data from stool and sputum samples. When I performed the ANCOM analysis in sputum data (comparing treatment vs. placebo) at phylum level, all phyla showed differences in abundance between treatment and placebo (but with low values for w and f in the vulcano plot). However, when I performed the same analysis in stool data, no by-phylum differences were encountered. I'm not sure if those results are related to errors from the data or incorrect approach. I attach here some results and the pipeline used. Thanks in advance!
Pipeline (for stool data):
qiime feature-table filter-samples --i-table results-dada2/tablef.qza --m-metadata-file metadata.tsv --p-where "Sample='stool'" --o-filtered-table differential-abundance/stool-tablef.qza
qiime taxa collapse --i-table differential-abundance/stool-tablef.qza --i-taxonomy taxon/taxonomy-gg.qza --p-level 2 --o-collapsed-table differential-abundance/stool-tablef-phylum.qza
qiime composition add-pseudocount --i-table differential-abundance/stool-tablef-phylum.qza --o-composition-table differential-abundance/comp-stool-tablef-phylum.qza
qiime composition ancom --i-table differential-abundance/comp-stool-tablef-phylum.qza --m-metadata-file metadata.tsv --m-metadata-column Treatment --o-visualization differential-abundance/l6-ancom-Subject-stoolf.qzv
metadata.tsv (5.5 KB)
taxonomy-gg.qza (82.1 KB)
l6-ancom-Subject-sputumf.qzv (331.6 KB)
l6-ancom-Subject-stoolf.qzv (330.9 KB)
tablef.qza (125.5 KB)