<p>I have different treatments (infected and control ones). When using DESeq2, I have different results in two ways of comparison.
first way:</p>
<p>factor: treatment, factor level1: Moribund Infected, factor level2: 5week Infected, factor level3: Moribund Control, factor level4: 5week Control.
I have 6 result files (comparisons among factor levels)</p>
<p>second way: (I compared just 2 groups to each other)</p>
<pre><code>factor: treatment, factor level1: Moribund Infected, factor level2: 5week Infected.
factor: treatment, factor level1: Moribund Infected, factor level2: Moribund Control.
factor: treatment, factor level1: Moribund Infected, factor level2:the  5week Control.
factor: treatment, factor level1: 5week Infected, factor level2: Moribund Control.
factor: treatment, factor level1: 5week Infected, factor level2: 5week Control.
factor: treatment, factor level 1: Moribund Control, factor level2: 5week Control.
</code></pre>
<p>Finally, the results were different in these two ways of comparison. I have more significantly expressed genes in most comparisons of first way and even I have few comparisons in the second way that have more significantly expressed genes.</p>
<p>Why and which way is trustable?</p>

CC BY-SA 4.0
2022-05-19T01:10:36.483Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2022-05-19T01:58:44.283Z
Could you please show the specific design formulas you used to describe the statistical models in the DESeq2 commands. Showing the full factor table would be helpful as well (e.g. `colData` in the DESeq2 commands).
gringer
CC BY-SA 4.0
2022-05-19T19:38:52.873Z
Cross-posted:https://support.bioconductor.org/p/9144330/
swbarnes2
<deseq2>
Different results of DESeq2 in different ways of comparison
# Different results of DESeq2 in different ways of comparison

(Asked by: username_0 on 2022-05-18)

I have different treatments (infected and control ones). When using DESeq2, I have different results in two ways of comparison.
first way:
factor: treatment, factor level1: Moribund Infected, factor level2: 5week Infected, factor level3: Moribund Control, factor level4: 5week Control.
I have 6 result files (comparisons among factor levels)
second way: (I compared just 2 groups to each other)
factor: treatment, factor level1: Moribund Infected, factor level2: 5week Infected.
factor: treatment, factor level1: Moribund Infected, factor level2: Moribund Control.
factor: treatment, factor level1: Moribund Infected, factor level2:the  5week Control.
factor: treatment, factor level1: 5week Infected, factor level2: Moribund Control.
factor: treatment, factor level1: 5week Infected, factor level2: 5week Control.
factor: treatment, factor level 1: Moribund Control, factor level2: 5week Control.

Finally, the results were different in these two ways of comparison. I have more significantly expressed genes in most comparisons of first way and even I have few comparisons in the second way that have more significantly expressed genes.
Why and which way is trustable?

**Tags:** deseq2
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Could you please show the specific design formulas you used to describe the statistical models in the DESeq2 commands. Showing the full factor table would be helpful as well (e.g. `colData` in the DESeq2 commands).  
> **username_3**: Cross-posted:https://support.bioconductor.org/p/9144330/  

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## 0 answers

