I'm actually running and trying to interpret ANCOM results. Briefly some important stuff about my data:
I'm working with microbiota from mosquitos midgut, I have 90 samples, I filtered my samples with a frequency like the depth chosed from the rarefaction that I used in diversity analysis (3800). Furthermore I filtered features with less than 10 reads and removed singletons.
So I runned ANCOM wiith one category from my metada ("local") and in this category I have 7 groups. I have more three categories, but I'm trying first to understand my preliminary results until step forward.
I've runned ANCOM with my filtered table and with the collapsed table (level 6) to compare results, for my surprising I have in both ANCOM volcano plot a too high W. I compared with others results from the Moving Pictures, Parkison's tutorial and in the forum. My W is very high and in my x-axis (F-score) I do not have negative numbers.
I don't know if this occurs normally, the ANCOM results from the collapsed table have a slightly smaller W.
Here I will post my code, and the files of the results from the filtered and collapsed-filtered table. But my questions are: There are some bias in my results? I can confirm which taxa (or features) are differentially abundant using the TSV table below as a parameter? Why my W it's too high?
qiime feature-table filter-samples \ --i-table filtered-table-trim-gg-decon.qza \ --p-min-frequency 3800 \ --o-filtered-table filtered-new-table.qza qiime feature-table filter-features \ --i-table filtered-new-table.qza \ --p-min-frequency 10 \ --p-min-samples 2 \ --o-filtered-table filtered-new-table-min10-samp2.qza qiime composition add-pseudocount \ --i-table filtered-new-table-min10-samp2.qza \ --o-composition-table filtered-new-table-min10-samp2_with_pseudocount.qza qiime composition ancom \ --i-table filtered-new-table-min10-samp2_with_pseudocount.qza \ --m-metadata-file Metadados.txt \ --m-metadata-column local \ --o-visualization ancom_local.qzv
qiime taxa collapse \ --i-table filtered-new-table-min10-samp2.qza \ --i-taxonomy taxonomy-gg.qza \ --p-level 6 \ --o-collapsed-table filtered_table_level-6.qza qiime composition add-pseudocount \ --i-table filtered_table_level-6.qza \ --o-composition-table filtered_table_level-6_with_pseudocount.qza qiime composition ancom \ --i-table filtered_table_level-6_with_pseudocount.qza \ --m-metadata-file Metadados.txt \ --m-metadata-column local \ --o-visualization ancom_collapsed_local.qzv