Hi! Just wondering if maaslin is currently able to handle nested random effects? I saw a post from Oct '20 mentioning they were not yet supported, but was wondering if they have been included since then. (In our dataset we have stool samples that are categorized into four different conditions, with four to five technical replicates of each). Thanks!
Sorry, I don’t believe nested random effects are supported.
No problem, thanks for the response!
How have other people treated technical replicates when using MaAsLin? I was considering combining the replicates in R before creating the MaAsLin model because using only the replicate with the highest read count feels like throwing away data.
Are nested effects still unsupported in Maaslin2?
Hi @acpoole,
Maaslin2 still does not support nested effects. Depending on your study you may be able to get away with just using the lowest nested effect as a your random effect.
Thanks,
Jacob