# Q-values on produced graphs and 'significant\_results.tsv' not lining up **URL:** \ **Category:** MaAsLin\ **Created:** [February 3, 2026, 5:06pm UTC](https://forum.biobakery.org/t/q-values-on-produced-graphs-and-significant-results-tsv-not-lining-up/8754 "2026-02-03T17:06:04Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![hah0024](https://avatars.discourse-cdn.com/v4/letter/h/bbe5ce/32.png) [@hah0024](https://forum.biobakery.org/u/hah0024)\ **Post date:** [February 3, 2026, 5:06pm UTC](https://forum.biobakery.org/t/q-values-on-produced-graphs-and-significant-results-tsv-not-lining-up/8754/1 "2026-02-03T17:06:04Z")
Hello! Thanks so much for making Maaslin3! I am really liking it so far, but had a question about a discrepancy i found within some of my outputs. Not all of the line graphs that are produced and labeled with a significant q-value are within the significant\_results.tsv. For example, see the Maaslin3 produced graph i’ve linked below (it’s a weird looking one but also the reason i used as an example). This particular OTU is shown to have an FDR qval of 3.1e-02. However, when i find it in the ‘all\_results.tsv’ this is the info given for it, not exactly lining up. It is not for all of them, as some of them do indeed match up between graphs and text files in terms of qvalues – so is it because of some correction, etc that the qvalues are changing between the produced graphs and the text files? Sorry, i hope this makes sense! Thanks for your help in advance! ![AST_OTU025_linear](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/1/1e7c98b8fd5e209b6222c7b4226e45d0ba932175.png) | feature | metadata | value | name | coef | null\_hypothesis | stderr | pval\_individual | qval\_individual | pval\_joint | qval\_joint | error | model | N | N\_not\_zero | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | OTU025 | AST | AST | AST | -1.3981705 | 0.05880495 | 0.40257938 | 0.00043592 | 0.08785455 | 0.00043592 | 0.06795249 | NA | abundance | 247 | 205 | My maaslin command: `fit_out ← maaslin3(` `input_data = bacteria,` `input_metadata = metadata,` `output = output_dir,` `normalization = “NONE”, ##Samples are already TSS` `transform = “LOG”,` `formula = "~ Treatment + AST + AST:Treatment + (1|Batch),` `augment = TRUE,` `standardize = TRUE,` `max_significance = 0.05,` `median_comparison_abundance = TRUE,` `min_abundance = 0.0001,` `min_prevalence = 0.1,` `max_pngs = 100,` `save_models = TRUE` ) ---
**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 3, 2026, 5:46pm UTC](https://forum.biobakery.org/t/q-values-on-produced-graphs-and-significant-results-tsv-not-lining-up/8754/2 "2026-02-03T17:46:54Z")
Just a quick sanity check - is that plot the same one you got from the MaAsLin command you pasted below? The plot says normalization TSS but the command says NONE. ---
**Author:** ![hah0024](https://avatars.discourse-cdn.com/v4/letter/h/bbe5ce/32.png) [@hah0024](https://forum.biobakery.org/u/hah0024)\ **Post date:** [February 3, 2026, 5:50pm UTC](https://forum.biobakery.org/t/q-values-on-produced-graphs-and-significant-results-tsv-not-lining-up/8754/3 "2026-02-03T17:50:29Z")
Alright, i think i may know what happened. Wow! I reran this with slightly different parameters previously, and it looks like some of those graphs were not removed and stayed in the directory. I think that explains the discrepancy 😆 . This was one of those graphs. If i look at just the ones that were made with this most recent run, they are correct. ---
**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 3, 2026, 6:01pm UTC](https://forum.biobakery.org/t/q-values-on-produced-graphs-and-significant-results-tsv-not-lining-up/8754/4 "2026-02-03T18:01:31Z")
Phew - glad to hear!