# Gneiss missing first parameter

**URL:** <https://forum.qiime2.org/t/gneiss-missing-first-parameter/3370>\
**Category:** User Support\
**Tags:** gneiss\
**Created:** [March 9, 2018, 4:26am UTC](https://forum.qiime2.org/t/gneiss-missing-first-parameter/3370 "2018-03-09T04:26:43Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jjmmii](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/j/f475e1/32.png) [@jjmmii](https://forum.qiime2.org/u/jjmmii)\
**Post date:** [March 9, 2018, 4:26am UTC](https://forum.qiime2.org/t/gneiss-missing-first-parameter/3370/1 "2018-03-09T04:26:43Z")

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I'm looking at regression\_summary.qzv on my own data generated following the gneiss tutorial [here](https://docs.qiime2.org/2018.2/tutorials/gneiss/) and noticed that the first parameter in each variable (each column in metadata) is missing. For example I have subjects labelled P1, P2, P3 ... Pn but P1 is missing. I also have groups C, W, P, and M but C is missing. Is this intended, and if so, why? Thank you very much.

-Jamie

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**Author:** ![mortonjt](https://forum.qiime2.org/user_avatar/forum.qiime2.org/mortonjt/32/3488_2.png) [@mortonjt](https://forum.qiime2.org/u/mortonjt)\
**Post date:** [March 9, 2018, 6:08am UTC](https://forum.qiime2.org/t/gneiss-missing-first-parameter/3370/2 "2018-03-09T06:08:14Z")

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There is a very similar question [here](https://forum.qiime2.org/t/gneiss-regression-summary-issue/2356).

If you are trying to fit a linear model with D categories, you will need to figure out a way to encode that model with D-1 contrasts. As a default, the first category is chosen as the reference contrast. We are using [patsy](http://patsy.readthedocs.io/en/latest/categorical-coding.html) to extract these design matrices, so it may be worthwhile to read the patsy documentation to figure out how to properly encode the formulas.

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**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\
**Post date:** [April 9, 2018, 12:08pm UTC](https://forum.qiime2.org/t/gneiss-missing-first-parameter/3370/3 "2018-04-09T12:08:33Z")

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