I have a short-chain fatty acid concentration table and I want to import the table to perform the procrustes-analysis with the microbiome sequencing data. Anyone knows how to import the table?
The table is like this:
sample-id acetate propionate butyrate iso-butyrate
sample1 3.4 2.1 2.0 0.4
sample2 2.5 1.8 1.6 0.3
sample3 2.1 1.9 1.2 0.1
sample4 20.4 14.3 17.3 1.2
sample5 15.4 19.9 17.4 2.1
sample6 25.3 23.2 15.3 3.2
In order to do what you want you’re going to need to import your table as a FeatureTable[Frequency] format since this is the format ultimately expected by the Procrustes plugin, which unfortunately means you can’t have non-integer values as it expects counts. One workaround would be to multiply all the values you have by 10 or 100 as to lose the decimal then you should be able to import it as a frequency table as you would normally. This tutorial should help with the importing. I have no idea if this is a valid approach for what you want to do, but it should work. Good luck!
Thank you for your prompt reply and help! I’ll try to import the data using the above method.