jwdebelius
April 27, 2020, 4:03pm
5
Sorry, I should have specifed better that I wanted to know what your question was, specifically, and then offered a list of potential questions. Im still not sure what you were trying to understand, but I'll link some of the Best of answers and maybe they'll help as a starting place. Then, you can always come back if there are more things you're not sure about.
Best,
Hi,
I would like to ask for a clarification for beta-group-significance results. I am comparing samples based on their origin. I evaluated weighted UniFrac beta-diversity metrics, and I plotted a PCoA. Based on that, and on taxonomic classification, I could clearly see samples from one origin being very different to samples from other two origins. Then I wanted to confirm this running a PERMANOVA test. Although the box and whisker plots confirm the results I got with the PCoA, I get all p-value…
Hi,
I have looked through the forum to the best of my ability to find answers to my questions, but have come up short on a few questions. I realize they are probably simple answers, but Qiime2 is new to me, and so is the statistics involved.
To quickly summarize my work, I have a collection of serum samples from aerosol challenged rhesus macaques that I tested with a serodiagnostic assay to look for immune responses. The serum samples can be categorized by collection date, such as pre-challeng…
Hi,
When I run the beta-group-significance script it is over-inflating the number of n's that I have in a sample group. I know these numbers can't be right because my whole dataset only has 98 samples (I'm looking at a subset that only encompasses 50 samples, the day 14 samples).
This is the script I ran:
qiime diversity beta-group-signfiicance --i-distance-matrix no_D0_core_metrics/weighted_unifrac_distance_matrix.qza --m-metadata-file ~/Desktop/Madison_seq_1/Jackson/jackson_mapping.txt --m…
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