I have analysed a time-series of samples, including 'q2 deicode rpca'. For some reasons, the samples of the latest time points, did not distribute along axis 1 and 2, but only on axis 3 (shown in the biplot for the latest 2 timepoints). If I analyse the latest timepoint alone, I get the samples distributed across the rpca plot as expected. I have attached both biplot.qzv packages.biplot.qzv (1.2 MB) biplot.qzv (1.2 MB)
The only obvious difference between data of different timepoints, that I see at the moment, is that the sequencing depth for the latest samples is considerably lower compared to the other sample. However, the samples were filtered before to remove low-abundant features. The taxa barplot was fine, and unifrac plots were also as expected.
I am using qiime2-2021.2 with the latest deicode/qurro plugins. (I have tested it with qiime2-2021.4, same results).
I would appreciate your comments.