Warning message: In var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) when running MaAsLin

Downstream analysis and statistics MaAsLin
1

Hello expert,

I tried to run MaAslin with my own data,
Here is the command:
fit_data = Maaslin2(
input_data = df_input_data,
input_metadata = df_input_metadata,
output = “demo_output3”,
analysis_method = “LM”,
fixed_effects = c(“Genotype”),
reference = c(“Genotype,XXF”),
normalization = “TSS”,
min_prevalence = 0,
min_abundance = 0)

After running, I received this warning:

2022-04-22 10:42:29 INFO::Creating boxplot for categorical data, Genotype vs EU791016_1_1501
2022-04-22 10:42:29 INFO::Creating boxplot for categorical data, Genotype vs CZPU01000011_139136_140633
2022-04-22 10:42:29 INFO::Creating boxplot for categorical data, Genotype vs AB702763_1_1498
2022-04-22 10:42:30 INFO::Creating boxplot for categorical data, Genotype vs DQ815763_1_1450
2022-04-22 10:42:30 INFO::Creating boxplot for categorical data, Genotype vs EU791016_1_1501
2022-04-22 10:42:30 INFO::Creating boxplot for categorical data, Genotype vs EU504667_1_1403
2022-04-22 10:42:30 INFO::Creating boxplot for categorical data, Genotype vs EU505531_1_1407
2022-04-22 10:42:31 INFO::Creating boxplot for categorical data, Genotype vs CZPU01000011_139136_140633
2022-04-22 10:42:31 INFO::Creating boxplot for categorical data, Genotype vs EU504667_1_1403
2022-04-22 10:42:31 INFO::Creating boxplot for categorical data, Genotype vs EU505531_1_1407
Warning message:
In var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) :
** NAs introduced by coercion**

Could you let me know how I can solve the current warning?

Thank you very much,

Kind regards,

Le Phuong Nguyen.

2

This error is probably due to some issue you with your input data, but it’s hard to tell without seeing the inputs. Did the fit finish and produce output figures/tables/etc for the other variables or did it stop when the warning occurred?