Hi. Is there any documentation of what the meaning is for each of the options for the arguments ‘analysis_method’, ‘normalization’ and ‘transform’? I have looked in several different places now, including the R manual, the tutorial at the huttenhower.sph… website, github, the github wiki and searched the mailing list and this forum. I’m sorry if I’ve overlooked it somewhere but for the life of me I cannot find a description.
Also, those sites give the manuscript in submission as the preferred citation for maaslin2. Is there a pre-print of that available anywhere that I can formally cite (or ideally also read before citing)? Is there a different citation that should be used in the interim? Thanks in advance for your help.
Hi @mgnute - apologies for the difficulty you faced while navigating the MaAsLin 2 manual. While we don’t have a publicly available preprint yet, I can point you to some relevant places where some or all of the information are available.
In particular, MaAsLin 2’s curated options are chosen based on a large-scale benchmarking of a combination of normalization/transformation and statistical models, which is publicly available here: https://github.com/biobakery/maaslin2_benchmark. This should give you some idea about the relevant benchmarking we did for the MaAsLin 2 validation.
For citation purposes, if you simply type citation('Maaslin2') in your R console after installing and loading the MaAsLin 2 package, you will find the relevant information there.
I hope this helps, but please let me know if you need anything else or if you have any other questions.