# Different p value in models\_linear.rds and significant\_results.tsv

**URL:** <https://forum.biobakery.org/t/different-p-value-in-models-linear-rds-and-significant-results-tsv/8804>\
**Category:** MaAsLin\
**Created:** [February 26, 2026, 1:06pm UTC](https://forum.biobakery.org/t/different-p-value-in-models-linear-rds-and-significant-results-tsv/8804 "2026-02-26T13:06:53Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Ben\_Tong](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ben_tong/32/2105_2.png) [@Ben\_Tong](https://forum.biobakery.org/u/Ben_Tong)\
**Post date:** [February 26, 2026, 1:06pm UTC](https://forum.biobakery.org/t/different-p-value-in-models-linear-rds-and-significant-results-tsv/8804/1 "2026-02-26T13:06:53Z")

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Hi!

I run Maaslin3 on my data with the code below

```r
otu_table1 <- ps %>% subset_samples(!is.na(Comparison1)) %>% otu_table() %>% as.data.frame()
metadata1 <- ps %>% subset_samples(!is.na(Comparison1)) %>% sample_data() %>% data.frame()
f1 <- paste0('Comparison1 + ', paste(covariates, collapse = '+'))

#================
#================
# Fit models
fit_out1 <- maaslin3(input_data = otu_table1,
                    input_metadata = metadata1,
                    output = '../../result/',
                    formula = f1,
                    normalization = 'TSS',
                    transform = 'LOG',
                    augment = TRUE,
                    standardize = TRUE,
                    max_significance = 0.1,
                    min_abundance = 0.0001,
                    min_prevalence = 0.1,
                    median_comparison_abundance = TRUE,
                    median_comparison_prevalence = FALSE,
                    max_pngs = 100,
                    cores = 10,
                    save_models = TRUE)

```

And it run without error. Though in the results folder, the p values I read from models\_linear.rds (1.545704e-04) for the significant correlation between a species _Dorea\_longicatena_ and a variable is not identical with their p value in significant\_results.tsv (p individual =1.316814e-05). But the coefficients are the same. Is it because they are calculated in different ways?

Best,

Ben

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**Author:** ![WillNickols](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/willnickols/32/3223_2.png) [@WillNickols](https://forum.biobakery.org/u/WillNickols)\
**Post date:** [February 26, 2026, 1:52pm UTC](https://forum.biobakery.org/t/different-p-value-in-models-linear-rds-and-significant-results-tsv/8804/2 "2026-02-26T13:52:32Z")

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Hi Ben,

The p-value in the rds file is from a comparison of the coefficient against 0, whereas the p-value in the significant results is from a comparison of the coefficient against the median since you have `median_comparison_abundance = TRUE` set. Does that explain what you’re seeing?

Will

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<div class="post-metadata">

**Author:** ![Ben\_Tong](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ben_tong/32/2105_2.png) [@Ben\_Tong](https://forum.biobakery.org/u/Ben_Tong)\
**Post date:** [February 27, 2026, 7:53am UTC](https://forum.biobakery.org/t/different-p-value-in-models-linear-rds-and-significant-results-tsv/8804/3 "2026-02-27T07:53:59Z")

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Yes, that’s very clear! Thank you!