Hello, I’m doing a maaslin3(version 1.0.0) analysis and my results show “All associations had errors or were insignificant”。 My code and data and result file
all_results (1).tsv (4.1 MB)
are as follows:
library(maaslin3)
packageVersion(“maaslin3”)
ph_TAN ← read.csv(“/data/work/QTP/maaslin3/TAN/Maaslin3_qtp_TA_255sample.csv”, head = TRUE, row.names = 1,check.names=FALSE)
SGB_TAN ← read.csv(“/data/work/QTP/maaslin3/TAN/qtp_TA_255sample_relabu.csv”, head = TRUE, row.names = 1,check.names=FALSE)
SGB_TAN ← SGB_TAN / 100
output_dir ← “/data/work/QTP/maaslin3/TAN/elevation_group/SGB”
input_TAN_data = as.data.frame(SGB_TAN)
input_TAN_metadata = as.data.frame(ph_TAN)
fit_out ← maaslin3(input_data = input_TAN_data,
input_metadata = input_TAN_metadata,
output = output_dir,
fixed_effects = c(“elevation_group”),
reference = c(“elevation_group,4-4.5KM”),
random_effects = c(“Latitude”, “Longitude”, “sampled_place”, “KP994558.1_s_Potentilla_acaulissta”, “KJ020646.1_s_Potentilla_parvifoliasta”, “MH854502.1_s_Fagopyrum_dibotryssta”, “HE577530.1_s_Chenopodium_hybridumsta”, “FJ640034.1_s_Leontopodium_pusillumsta”, “AB480625.1_s_Orostachys_fimbriatasta”, “KU750607.1_s_Senecio_scandenssta”),
normalization = “TSS”,
transform = “LOG”,
warn_prevalence = TRUE,
augment = TRUE,
standardize = TRUE,
max_significance = 0.1,
median_comparison_abundance = TRUE,
median_comparison_prevalence = FALSE,
max_pngs = 250,
cores = 10)
qtp_TA_255sample_relabu.csv (9.8 MB)
Maaslin3_qtp_TA_255sample.csv (29.7 KB)
Can you tell me what is the reason for this problem?
Best wishes