# Interaction terms in deseq2 and PCA plots

**URL:** <https://help.galaxyproject.org/t/interaction-terms-in-deseq2-and-pca-plots/18626>\
**Category:** Uncategorized\
**Created:** [November 11, 2026, 5:43pm UTC](https://help.galaxyproject.org/t/interaction-terms-in-deseq2-and-pca-plots/18626 "2026-11-11T17:43:11Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![microfuge](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/microfuge/32/3587_2.png) [@microfuge](https://help.galaxyproject.org/u/microfuge)\
**Post date:** [November 11, 2026, 5:43pm UTC](https://help.galaxyproject.org/t/interaction-terms-in-deseq2-and-pca-plots/18626/1 "2026-11-11T17:43:11Z")

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Hi ,

I was wondering if design formulas like `~ genotype + light + genotype:light` can be put in current galaxy deseq2 wrapper. Also in R one can just do a ` `~1 `` To get just the pca plot of all samples together.

These two things would be great for recommending galaxy at my workspace.

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**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\
**Post date:** [November 12, 2026, 9:01am UTC](https://help.galaxyproject.org/t/interaction-terms-in-deseq2-and-pca-plots/18626/2 "2026-11-12T09:01:00Z")

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Hi @microfuge

I created an issue here [DESeq2: add support for interaction effects · Issue #8907 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/8907)

But the implementation might take some time. If you have a colleague who can implement it, please share the following repo to contribute. We are happy to review 🙂

> **[tools-iuc/tools/deseq2 at main · galaxyproject/tools-iuc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2)**
>
> main/tools/deseq2

Thank you for understanding!

Pavan

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<div class="post-metadata">

**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\
**Post date:** [November 12, 2026, 9:25am UTC](https://help.galaxyproject.org/t/interaction-terms-in-deseq2-and-pca-plots/18626/3 "2026-11-12T09:25:18Z")

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Meanwhile, please try mimicking your formula with some changes to the input for the current DESeq2 wrapper.

- Use the input mode “Select contrast from sample sheet columns”
- Have your count files in a collection. Name each of the samples.
- Prepare a sample sheet file. In addition to light and genotype, add a column that defines the interaction. Something like the following

| sample | genotype | light | interaction |
| --- | --- | --- | --- |
| WT\_dark\_1 | WT | dark | no |
| WT\_dark\_2 | WT | dark | no |
| WT\_light\_1 | WT | light | no |
| WT\_light\_2 | WT | light | no |
| mutant\_dark\_1 | mutant | dark | no |
| mutant\_dark\_2 | mutant | dark | no |
| mutant\_light\_1 | mutant | light | yes |
| mutant\_light\_2 | mutant | light | yes |

Then use the formula `~ genotype + light + interaction`. I haven’t tested. That might work.