Closed alex-d13 closed 3 years ago
Hi Alex,
Thank you for your question! I can imagine that other people might have the same problem
I looked into your dataset and you seem to have percentages of taxa (each sample sums up to 100). SIAMCAT expects relative abundances (each sample sums up to 1). Either, you divide each column in your input matrix by 100 or you can use the prop.table
function in R:
feat.rel <- prop.table(feat, 2)
I hope this clears it up :) Cheers, Jakob
Hi, I want to run check.associations on my data and get the following error:
Error in check.associations(s.obj, fn.plot = NULL) : This function expects compositional data. Exiting...
My s.obj looks like this:
Here is my OTU table: https://www.dropbox.com/s/6b50yjnpy2udz5b/rel_abund.tsv?dl=0
Can you help me what is the issue here? Cheers, Alex