I have a bit of a weird situation where I had to re-sequence some of my samples due to some controls being positive on that particular plate, but then later found out that the original plate was actually labelled incorrect and my original sequences should be fine as long as I correct the label. I want to use my original samples in my analysis instead of the re-ran samples because the re-sequenced samples have a batch effect.
Now since my re-sequenced samples should show high similarity to the label corrected original sequences, I wanted to show that the label correct samples are closer to the re-sequenced samples than before the label correction as a way to show the problem was in fact just a problem with the label. I thought a good way of doing this would be to create two procrustes analysis plots one with the PCOA from the re-sequenced samples (reference) vs. PCOA of incorrect labels and the other plot with the PCOA from the re-sequenced samples vs. PCOA of correct labels to show the corrected labels are closer related to the re-sequenced than the incorrect labeled.
I have created distance matrices using the stand alone qiime diversity beta-phylogenetic so I could avoid using a sampling depth that could create mismatches of the samples in my matrices and then used those matrices to create pcoa plots. But when I try the qiime diversity procrustes-analysis I get an error message saying:
Plugin error from diversity:
The ordinations represent two different sets of samples
How does procrustes check my sample sets to determine they are different? And can I get it to make this comparison?