The bioBakery help forum

Warning message in Maaslin2


First, Maaslin2 is a really really wonderful tool!

I am running an analysis with one predictor of interest and 7 categorical covariates. I’ve run maaslin2 (lm analysis method, “AST” transformation, min prevalence and abundance thresholds to filter out rare features), and a warning message comes along with the output, saying “Warning message: In var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) : Calling var(x) on a factor x is deprecated and will become an error.” what would be the possible causes?

Thank you!

Hi @ayuhhh,

Thank you for your feedback. This warning looks like it is letting us know that soon the way we phrased something in the source code will no longer work. I will add this to our development document for a patch in the next release. Thank you for sharing it with us. I do not believe that this will change anything about how MaAsLin is currently running… but if you want to share your data (or a minimally reproducible/blinded dataset) I am happy to take a closer look.


Thanks for your reply. My R code for the Maaslin analysis was as follows:

fit_data ← Maaslin2(
input_data1, input_metadata1,‘demo_output’, transform = “AST”,
max_significance = 0.1,
fixed_effects = c(“status”),
normalization = ‘NONE’,
reference = c(‘status,HC’))

and the input_data file and the input_metadata file were attached.input_data.csv (627.3 KB)
input_metadata.csv (852 Bytes)

Looking forward to your reply. Thanks!