Hi all,
I have two different primer sets that have been used to amplify the same sample set. I want to do a Procrustes analysis to see if the primers generate a difference in the alpha or beta diversity. I have successfully generated PCoAResults files for both data sets. Unfortunately, when I attempt to use my two PCoAResults files as input for the qiime diversity procrustes-analysis function I get the following error The matrices cannot be fitted unless they have the dimensions and samples. I have very little stats knowledge, so I don't understand what this error is telling me. Would appreciate insight into what I am doing wrong and how I can correct this problem. Thanks so much!
Hi @AlfalfaResearcher, thanks for reporting this problem.
The problem here is that the matrices you are trying to fit don't have the same dimensions. This would usually happen if one or more of the samples were dropped out during rarefaction or weren't processed with both primer sets. If this is the case, then you could make the matrices comparable by filtering them to include the same samples, see qiime diversity filter-distance-matrix.
The error message is confusing, I've fixed this in the code so it should be clearer for the next release 
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Hi @yoshiki,
Thank you so much for clarifying this for me! I'll try what you recommend and I'll watch for the next release.
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