Hi dear qiime community,
I used the qiime longitudinal volatility command on the faith-pd vector data for a pairwise comparison between two conditions: Pre versus Post treatment, whereas for each patient I have these two samples (pre and post).
Unfortunately, although I got a nice visualization plot thanks to this platform, I can’t find any significancy out of it.
Is there a significance command that I need to do to get significance value? Like the command
qiime diversity alpha-group-significance we are using on the .qza files in the core directory for the specific alpha diversity needed? My problem with the
qiime longitudinal volatility command is that the output files are already in a .qzv format.
When I tried to use the
qiime diversity alpha-group-significance command on the
qiime longitudinal volatility output, I got this expected error comment:
(1/1) Invalid value for '--i-alpha-diversity': '../Desktop/Pre_Post_analysis/ without_eggs/Pre_Post_250721/core_10000_filtered_merged_table_feature- frequency_no_plant_taxa_NO_eggs_no_low_reads_samples_pairs-PRE_POST_No_contr ol_analysis_250721/faith_pd_vector_volatility_pairwise_Pre_or_Post_0_1.qzv' is a QIIME 2 visualization (.qzv), not an Artifact (.qza)
So, what am I missing? Maybe I need to use another command for significance?
Or do I need to use the faith-pd values I got for each specific sample and do the pairwise calculation by myself somehow? (I can see the faith-pd values for each sample on the data I exported as TSV from the
qiime longitudinal volatility output).
Note that I am specifically interested in the pairwise differences, comparing the differences between pre and post treatment conditions in patients, but in a pairwise manner.
Thank you in advance!
I am currently running qiime2-2021.4 version installed on conda env on my mac.
This is my command (sorry for the long names):
qiime longitudinal volatility \ --m-metadata-file ../Desktop/Pre_Post_analysis/mf/mf_pre_post_June_2021_Hadar_with_controls_numeric_180821_0_1.tsv \ --m-metadata-file ../Desktop/Pre_Post_analysis/without_eggs/Pre_Post_250721/core_10000_filtered_merged_table_feature-frequency_no_plant_taxa_NO_eggs_no_low_reads_samples_pairs-PRE_POST_No_control_analysis_250721/faith_pd_vector.qza \ --p-default-metric faith_pd \ --p-default-group-column Pre_or_Post \ --p-state-column Pre_or_Post_numeric \ --p-individual-id-column Subject_code \ --o-visualization ../Desktop/Pre_Post_analysis/without_eggs/Pre_Post_250721/core_10000_filtered_merged_table_feature-frequency_no_plant_taxa_NO_eggs_no_low_reads_samples_pairs-PRE_POST_No_control_analysis_250721/faith_pd_vector_volatility_pairwise_Pre_or_Post_0_1.qzv \