# Output All results N.not.0=0 **URL:** \ **Category:** MaAsLin\ **Created:** [July 6, 2020, 5:38am UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673 "2020-07-06T05:38:34Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Anne](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anne](https://forum.biobakery.org/u/Anne)\ **Post date:** [July 6, 2020, 5:38am UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673/1 "2020-07-06T05:38:34Z")
When I look at the output i get using Maaslin2, the column N.not.0 in the significant results file for all of my bacterial species is 0. The column is all 0 even in the file listing bacterial species which do not have significant associations with the variables I’m testing for. I do not understand why I am getting this output particularly when the input data in my taxonomy table looks normal and a good proportion of my data is not 0. I get the same problem even when using the demo data from the Maaslin2 tutorial using the code below. ![Screenshot 2020-07-06 17.31.23](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/c99d98dceeb04473b19a575a4a765e53922c2bac.png) library(Maaslin2) input\_data = system.file( “extdata”, “HMP2\_taxonomy.tsv”, package=“Maaslin2”) input\_metadata = system.file( “extdata”, “HMP2\_metadata.tsv”, package=“Maaslin2”) df\_input\_data = read.table(file = input\_data, header = TRUE, sep = “\t”, row.names = 1, stringsAsFactors = FALSE) df\_input\_metadata = read.table(file = input\_metadata, header = TRUE, sep = “\t”, row.names = 1, stringsAsFactors = FALSE) fit\_data = Maaslin2( input\_data = input\_data, input\_metadata = input\_metadata, output = “demo\_output”, fixed\_effects = c(“diagnosis”, “dysbiosis”)) Does anyone have some insight on why this is happening? Thank you Anne ---
**Author:** ![sma](https://avatars.discourse-cdn.com/v4/letter/s/dec6dc/32.png) [@sma](https://forum.biobakery.org/u/sma)\ **Post date:** [July 10, 2020, 3:23pm UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673/2 "2020-07-10T15:23:15Z")
Hi - Thanks for bringing this to our attention. I believe this is a bug when running Maaslin2 using the `"LOG"` transformation (the default). Maaslin2 adds a pseudo count before taking log transformation to accommodate zeros, which causes it to count non-zero values incorrectly. I’ll report this to the developers. Best, Siyuan ---
**Author:** ![Anne](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anne](https://forum.biobakery.org/u/Anne)\ **Post date:** [July 11, 2020, 2:56am UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673/3 "2020-07-11T02:56:43Z")
Hi Siyuan Thank you for the reply! I just also wanted to add that I got the N.not.0 error (as well incorrect significant results/incorrect figures/incorrect Y axis on my figures) when running it on R-4.0.2. but did not get the same problem when running the code on R-3.6.0. When using R-3.6.0 the output I get using the demo Maaslin2 tutorial data is all correct. I’m not how, but the problem may have something to do with the version of R installing and running MaAslin2. Thanks Kind Regards Leanne ---
**Author:** ![Lyoon6](https://avatars.discourse-cdn.com/v4/letter/l/7ea924/32.png) [@Lyoon6](https://forum.biobakery.org/u/Lyoon6)\ **Post date:** [October 7, 2020, 2:36pm UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673/4 "2020-10-07T14:36:19Z")
Hi Siyuan, I am also getting this problem in all results (not just significant ones). Was this bug fixed? What might be a workaround for fixing it? Thanks! Lara ---
**Author:** ![himel.mallick](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/himel.mallick/32/1757_2.png) [@himel.mallick](https://forum.biobakery.org/u/himel.mallick)\ **Post date:** [October 7, 2020, 9:52pm UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673/5 "2020-10-07T21:52:03Z")
Hi @Lyoon6 - my impression is that it has been fixed. Can you install the development version from GitHub and see if that changes your results? ---
**Author:** ![Lyoon6](https://avatars.discourse-cdn.com/v4/letter/l/7ea924/32.png) [@Lyoon6](https://forum.biobakery.org/u/Lyoon6)\ **Post date:** [December 1, 2020, 6:04am UTC](https://forum.biobakery.org/t/output-all-results-n-not-0-0/673/6 "2020-12-01T06:04:01Z")
Hello, Yes- this fixed it! Thanks.