Hi, all.
I used dist.shared() to calculate the distances of OTU memberships or structures.
I tried the calculators found in mothur wiki, but several ones give negative values.
canberra gower helinger mahattan whittaker structeuclidean structchord structochiai hamming kulczynski memeuclidean memchord structchi2 spearman
ps: The .shared file I used is just the output file from cluster(), and the other Membership and Structure calculators give no negative values.
Bai
Bai,
Sorry about this and thanks for bringing it to our attention. These will be fixed in the next release. If you need these, please email us and we can get you an updated copy of the source code. The problem primarily stemmed from us subtracting these values from 1 to get a distance when the values were already distances and were not bounded between 0 and 1.
Pat
Hi, Prof. Schloss, it’s very kind of you to answer my question. I think I have got your point.
I am very glad to try the new release of Mothur and I will send an Email to ask for it.
Best wishes.
Bai
I am still seeing negative values with Whittaker. e.g. summary.shared(calc=whittaker)
I thought I might be able to just add 1, but the values range from -3 to -236. Weird.
mothur v.1.27.0
Mac 10.7.5
Can you email us a shared file with what samples are giving you negative values?