The bioBakery help forum

Reference option missing in the latest MaAsLin2 R package


I was following the tutorial (MaAsLin2 · biobakery/biobakery Wiki · GitHub) to run the demo data provided with the package. However, with every fit_data I found the same error shown up. It seems the latest R package does not include the ‘reference’ option anymore. How does this affect the analysis using MaAslin2 as applied to categorical metadata?

One of the error messages is attached below as an example:

fit_data_random = Maaslin2(
input_data = df_input_data,
input_metadata = df_input_metadata,
output = “demo_output_random”,
fixed_effects = c(“diagnosis”, “dysbiosis”),
random_effects = c(“subject”),
reference = c(“diagnosis,nonIBD”))

Error in Maaslin2(input_data = df_input_data, input_metadata = df_input_metadata, : **
** unused argument (reference = c(“diagnosis,nonIBD”))

Thank you for your help in advance.


Hi @Shuqi_Li,

To start can I check which version of MaAsLin are you using?


Hi Kelsey,

[1] ‘1.2.0’

Thank you!

Hi @Shuqi_Li,

It looks like you have an older version of MaAsLin - the current Bioconductor version is at 1.6.0 can you upgrade the package and try again? I believe you have the version before we implemented the reference call.

Let me know if that doesn’t work!