I’m trying to run the differential abundance script on my data and have run into some issues. I am trying to use one of the statistical methods other than f_oneway and I receive errors for the others:
mannwhitneyu: Plugin error from composition:
alternative should be None, ‘less’, ‘greater’ or ‘two-sided’
wilcoxon: Plugin error from composition:
Zero method should be either ‘wilcox’ or ‘pratt’ or ‘zsplit’
kruskal: Plugin error from composition:
All numbers are identical in kruskal
I’m unsure how to fix the parameters (alternative and Zero method) and I looked at the frequency table and all the numbers are not identical, so I’m unsure why kruskal is having problems. I did notice that there is a cmd-config option in the help of the script. Is this file similar to the parameters file from QIIME 1? If so, could I get an example file to base mine off of?
Hi @saatkinson, can you please provide an example of how you are attempting to run this step? Copy-and paste from your terminal is fine. Also, please note we are planning on releasing QIIME 2 2017.7 this week, which drops q2-composition, in favor of q2-gneiss, which uses the gneiss software package. Thanks!
Hi @saatkinson! It looks like you identified some bugs here (it appears that some of the non-default stats aren’t wired up correctly in q2-composition, I was able to independently reproduce your reported errors). At this point we aren’t going to worry about fixing this, because as I mentioned earlier, QIIME 2 2017.7 will drop q2-composition in favor of q2-gneiss. Thank you so much for reporting this, I am sorry the outcome isn’t more satisfying, but we are really excited about q2-gneiss!
ANCOM isn’t included in q2-gneiss; q2-gneiss provides its own methods for differential abundance analysis. There will be a q2-gneiss tutorial posted on the forum soon, and the tutorial will be integrated into the QIIME 2 docs during the next release cycle. Stay tuned!
Hi @vrbana: at this time we aren’t planning on continuing to support ANCOM in the officially distributed plugins. Pinging @mortonjt to comment on the benefits of utilizing the differential abundance methods available in the new q2-gneiss plugin. I also recommend looking at the gneiss docs, to learn more about the differential abundance methods implemented there (q2-gneiss is a wrapper plugin around gneiss). Please let us know if you have any questions!
Since QIIME 2 is decentralized, a plugin developer that is interested in developing their own plugin that implements ANCOM is a real possibility — this is actually one of the main reasons that QIIME 2 is decentralized! We have left the deprecated plugin code up and available if anyone is interested in forking it. Thanks!