Comments (4)
Thanks for your question, @whats-in-the-box!
I have realized this bug (yes, you caught a bug!). The reason is that some taxa are very rare (some may only have one observation) and the variance estimation will fail in these rare taxa. Thus, the problem will be gone when you aggregate the table to higher taxonomic levels, simply because you make the count table denser.
I will correct this bug and release a new version of ancombc
function soon (probably next month). Meanwhile, you can try a more stringent filter to filter out rare taxa (e.g. set zero_cut = 0.8
instead of 0.9
) at this moment.
Best,
Huang
from ancombc.
I would like to bring to your awareness that we have just released a new update of ANCOMBC (1.6.1) R package. Hopefully, you will find this version works more smoothly.
Best,
Huang
from ancombc.
Hello!
I am using v 1.6.2 and got the same error.
from ancombc.
Hi @camilagazolla,
Are there any other warning messages?
Please note that in ANCOMBC 1.6.2, zero_cut
has been replaced with prv_cut
, and prv_cut = 1 - zero_cut
.
Best,
Huang
from ancombc.
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from ancombc.