Maaslin2 does not retrieve any figure nor significant result

Downstream analysis and statistics MaAsLin
1

Hi, I am running Maaslin2 in RStudio with microbial relative abundances.
However, when I run different comparisons I get no errors, but no significant results or figures are represented. I don’t know if I am doing something wrong. Please find attached the metadata and sample data. Thanks in advance.

genus_table_rel_OS_MMA.tsv (317.3 KB)
sample_metadata_MMA.tsv (2.7 KB)

input_data = system.file(“extdata”, “genus_table_rel_OS_MMA.tsv”, package=“Maaslin2”) # The abundance table file input_data
input_metadata = system.file(“extdata”, “sample_metadata_MMA.tsv”, package=“Maaslin2”) # The metadata table file input_metadata

df_input_data = read.table(file = input_data,
header = TRUE,
sep = “\t”,
row.names = 1,
stringsAsFactors = FALSE)
df_input_data[1:5, 1:5]
df_input_metadata = read.table(file = input_metadata,
header = TRUE,
sep = “\t”,
row.names = 1,
stringsAsFactors = FALSE)
df_input_metadata[1:5, ]

fit_data = Maaslin2(input_data = input_data,
input_metadata = input_metadata,
min_prevalence = 0,
normalization = “NONE”,
output = “OS_MMA_retro”,
fixed_effects = c(“OS”),
reference = c(“OS,LTS”))

fit_data2 = Maaslin2(input_data = input_data,
input_metadata = input_metadata,
normalization = “NONE”,
output = “OS_MMA_retro2”,
fixed_effects = c(“OS”),
reference = c(“OS,STS”),
min_prevalence = 0,
min_abundance = 0.00000000001)

2

Hello @JUAN_VICENTE_VALOR

I would check in your output folder the file all_results.tsv this should contain all of the model coefficients and p-values that were obtained by MaAsLin2. Depending on your study, and the fdr cutoff you choose it might be possible that none of the features in your genus table passed the q-value threshold.

Cheers,
Jacob

3

Dear @nearinj, thank you for your response. I went directly to significant_results.tsv, but you are right: there is information in all_results.tsv. I managed to get figures increasing the max_significance parameter of the code. Thanks a lot,

Juan

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