Qiime diversity - error message on the input distance matrix

After running qiime diversity beta-group-significance, the output shows that 2 samples were filtered out from the input distance matrix.
How to verify which samples are filtered out? Is there a way to examine the matrix?

Hi @Hind_Sbihi,

Great question! I am actually kind of surprised that we don’t indicate which samples were removed, so there isn’t a good way to tell from the visualization itself.

This part is a little more straight-forward, you should be able to run something like:

qiime tools export path/to/distance-matrix.qza --output-dir exported-dm/ 

You’ll see a file in “exported-dm” (or whatever you choose to name that directory) called distance-matrix.tsv. You should be able to open that in your favorite spreadsheet editor and cross-reference the IDs with your metadata. Sorry there isn’t a better way at the moment.

I’ve also created an issue to put the filtered IDs somewhere in the output (or error with the missing IDs).



Thanks a bunch Evan! Looking forward to further development. This was very helpful

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.