I do have 5 columns in metadata file: SampleID, Tissue (soil, root, shoot), Treatment (T1, T2, T3), Village and Region for all sample.
there are 3 tissue: soil, root and leaf.
I wanted to see differential abundance in all soil sample. I think I am making error in giving --P-where parameter, could you please suggest How should I correct it.
I used below command to filter and further process:
[qiime2_16s_analysis]$ qiime feature-table filter-samples --i-table table.qza --m-metadata-file metadata3.tsv --p-where “Tissue=‘Soil’” --o-filtered-table Soil-table.qza
Saved FeatureTable[Frequency] to: Soil-table.qza
qiime2_16s_analysis]$ qiime composition add-pseudocount --i-table Soil-table.qza --o-composition-table com-Soil-table.qza
Saved FeatureTable[Composition] to: com-Soil-table.qza
[qiime2_16s_analysis]$ qiime composition ancom --i-table com-Soil-table.qza --m-metadata-file metadata3.tsv --m-metadata-column Tissue --o-visualization ancom-Soil.qzv
Plugin error from composition:
All values the
grouping are the same. This method cannot operate on a grouping vector with only a single group of samples(e.g., there are no ‘between’ variance because there is only a single group).
Debug info has been saved to /tmp/qiime2-q2cli-err-hvbdjtm7.log