# Maaslin2 does not retrieve any figure nor significant result

**URL:** <https://forum.biobakery.org/t/maaslin2-does-not-retrieve-any-figure-nor-significant-result/7527>\
**Category:** MaAsLin\
**Created:** [October 29, 2024, 11:01am UTC](https://forum.biobakery.org/t/maaslin2-does-not-retrieve-any-figure-nor-significant-result/7527 "2024-10-29T11:01:06Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![JUAN\_VICENTE\_VALOR](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/juan_vicente_valor/32/2876_2.png) [@JUAN\_VICENTE\_VALOR](https://forum.biobakery.org/u/JUAN_VICENTE_VALOR)\
**Post date:** [October 29, 2024, 11:01am UTC](https://forum.biobakery.org/t/maaslin2-does-not-retrieve-any-figure-nor-significant-result/7527/1 "2024-10-29T11:01:06Z")

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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](https://forum.biobakery.org/uploads/short-url/u0rBGUUbMHqddCX0mkrfHw2KyLk.tsv) (317.3 KB)  
[sample\_metadata\_MMA.tsv](https://forum.biobakery.org/uploads/short-url/tWkrMXDvlDQRzy5DNFCJVw7ciW7.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)

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**Author:** ![nearinj](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nearinj/32/2135_2.png) [@nearinj](https://forum.biobakery.org/u/nearinj)\
**Post date:** [October 29, 2024, 4:06pm UTC](https://forum.biobakery.org/t/maaslin2-does-not-retrieve-any-figure-nor-significant-result/7527/2 "2024-10-29T16:06:33Z")

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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

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**Author:** ![JUAN\_VICENTE\_VALOR](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/juan_vicente_valor/32/2876_2.png) [@JUAN\_VICENTE\_VALOR](https://forum.biobakery.org/u/JUAN_VICENTE_VALOR)\
**Post date:** [October 30, 2024, 8:41am UTC](https://forum.biobakery.org/t/maaslin2-does-not-retrieve-any-figure-nor-significant-result/7527/3 "2024-10-30T08:41:53Z")

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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