# Using CONQUR-corrected matrices in MaAsLin 3

**URL:** <https://forum.biobakery.org/t/using-conqur-corrected-matrices-in-maaslin-3/9051>\
**Category:** MaAsLin\
**Created:** [September 4, 2026, 3:25pm UTC](https://forum.biobakery.org/t/using-conqur-corrected-matrices-in-maaslin-3/9051 "2026-09-04T15:25:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Esther\_Crivelli\_Gali](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/esther_crivelli_gali/32/3720_2.png) [@Esther\_Crivelli\_Gali](https://forum.biobakery.org/u/Esther_Crivelli_Gali)\
**Post date:** [September 4, 2026, 3:25pm UTC](https://forum.biobakery.org/t/using-conqur-corrected-matrices-in-maaslin-3/9051/1 "2026-09-04T15:25:23Z")

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Hi BioBakery Team,

We pre-corrected our raw microbiome count matrices for batch effects using **CONQUR**. We are now analyzing associations with clinical outcomes using **MaAsLin 3**.

To validate our pipeline, should we omit `Batch` from the MaAsLin 3 formula given the prior CONQUR correction, and are `normalization = 'TSS'` and `transform = 'LOG'` still the appropriate settings for this adjusted input?

Thanks for your support!

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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:** [September 5, 2026, 5:16am UTC](https://forum.biobakery.org/t/using-conqur-corrected-matrices-in-maaslin-3/9051/2 "2026-09-05T05:16:06Z")

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Hi,

The outputs you get from CONQUR should be similar to what we usually get with MMUPHin. With MMUPHin (and therefore presumably with CONQUR), we usually use TSS, LOG, and we still include a random effect per-batch in the regression in case there’s dependence leakiness.

Will