Hi there, I have successfully run MaAsLin on a dataset of 408 human microbiome samples using the attached metadata file and feature table. Currently I’m looking at just 1 variable in the metadata file (“source”) and I have set a reference for this variable. As you can see below, the code works but then I receive a message that there are no associations to plot. I find this hard to believe, and wonder if the problem stems from the warnings that I receive (see below).

Any advice? I’m not sure if there is something going on with my dataset, or perhaps a different parameter to tweak in the code?

Many thanks,

Melissa

taxa = read.delim(“maaslin_feature_table2_trimzero_a.txt”, sep = “\t”, row.names = 1)

taxa = data.frame(t(taxa), check.names = F)

meta = read.delim(“maaslin_metadata_merged_T2a_source.txt”, sep = “\t”, row.names = 1)

meta = data.frame(t(meta), check.names = F)

fit_data = Maaslin2(taxa, meta, “my_output”, transform = “AST”,

fixed_effects = c(‘source’),

reference = c(‘source,infant’),

normalization = “NONE”,

standardize = F,

min_prevalence = 0.1,

min_abundance = 0.001)

#It seems to run alright, but then I receive the message:

[1] “There are no associations to plot!”

There were 50 or more warnings (use warnings() to see the first 50)

#If I check on the warnings, I see this:

warnings()

Warning messages:

1: In asin(sqrt(abs(x))) : NaNs produced

2: In asin(sqrt(abs(x))) : NaNs produced

3: In asin(sqrt(abs(x))) : NaNs produced

4: In asin(sqrt(abs(x))) : NaNs produced

5: In asin(sqrt(abs(x))) : NaNs produced

6: In asin(sqrt(abs(x))) : NaNs produced

7: In asin(sqrt(abs(x))) : NaNs produced

8: In asin(sqrt(abs(x))) : NaNs produced

9: In asin(sqrt(abs(x))) : NaNs produced

10: In asin(sqrt(abs(x))) : NaNs produced

11: In asin(sqrt(abs(x))) : NaNs produced

12: In asin(sqrt(abs(x))) : NaNs produced

13: In asin(sqrt(abs(x))) : NaNs produced

14: In asin(sqrt(abs(x))) : NaNs produced

15: In asin(sqrt(abs(x))) : NaNs produced

16: In asin(sqrt(abs(x))) : NaNs produced

17: In asin(sqrt(abs(x))) : NaNs produced

18: In asin(sqrt(abs(x))) : NaNs produced

19: In asin(sqrt(abs(x))) : NaNs produced

20: In asin(sqrt(abs(x))) : NaNs produced

21: In asin(sqrt(abs(x))) : NaNs produced

22: In asin(sqrt(abs(x))) : NaNs produced

23: In asin(sqrt(abs(x))) : NaNs produced

24: In asin(sqrt(abs(x))) : NaNs produced

25: In asin(sqrt(abs(x))) : NaNs produced

26: In asin(sqrt(abs(x))) : NaNs produced

27: In asin(sqrt(abs(x))) : NaNs produced

28: In asin(sqrt(abs(x))) : NaNs produced

29: In asin(sqrt(abs(x))) : NaNs produced

30: In asin(sqrt(abs(x))) : NaNs produced

31: In asin(sqrt(abs(x))) : NaNs produced

32: In asin(sqrt(abs(x))) : NaNs produced

33: In asin(sqrt(abs(x))) : NaNs produced

34: In asin(sqrt(abs(x))) : NaNs produced

35: In asin(sqrt(abs(x))) : NaNs produced

36: In asin(sqrt(abs(x))) : NaNs produced

37: In asin(sqrt(abs(x))) : NaNs produced

38: In asin(sqrt(abs(x))) : NaNs produced

39: In asin(sqrt(abs(x))) : NaNs produced

40: In asin(sqrt(abs(x))) : NaNs produced

41: In asin(sqrt(abs(x))) : NaNs produced

42: In asin(sqrt(abs(x))) : NaNs produced

43: In asin(sqrt(abs(x))) : NaNs produced

44: In asin(sqrt(abs(x))) : NaNs produced

45: In asin(sqrt(abs(x))) : NaNs produced

46: In asin(sqrt(abs(x))) : NaNs produced

47: In asin(sqrt(abs(x))) : NaNs produced

48: In asin(sqrt(abs(x))) : NaNs produced

49: In asin(sqrt(abs(x))) : NaNs produced

50: In asin(sqrt(abs(x))) : NaNs produced

maaslin_metadata_merged_T2a_source.txt (6.7 KB)

maaslin_feature_table2_trimzero_a.txt (55.1 KB)