As I understand the compute-comparison tool only works with daa or rma files.
After running taxonomy2function I will get one .txt per sample. These txt files need to be merged to one joint table. Taxonomy2 function does this already when l being run as one command on multiple samples, but now gives the java error.
The function to join the tables was added in version 21.16: Taxonomy2function suggestions - #2 by Daniel
But i am not sure how this is done if i run each sample separately using taxonomy2 function.