beta diversity

[Ana Rabaza]

Hello:

I am trying to calculate the beta diversity and I have this problem.

Script:

qiime@qiime-190-virtual-box:~/Downloads/LR$ beta_diversity_through_plots.py -i otu_table_no_singletons_no_chimeras.biom -m MappingFile.txt -o wf_bdiv_even20000/ -t rep_set.tre -e 20000

Error:

/usr/local/lib/python2.7/dist-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:107: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.0992647323676 and the largest is 1.67869555754.

  RuntimeWarning

Can someone help me please?

Ana.

[Jamie Morton]

Hi Ana,

Do you have output for this data?  It looks like you are just getting a warning, and in your case your smallest eigenvalue is pretty close to zero.

So it may not be a problem.

Best,

Jamie