Question: DESEq2 comparison with two conditions and paired experiments
gravatar for severine.vincent
5.1 years ago by
European Union
severine.vincent0 wrote:


I have a question about an analysis of RNA seq data via DESeq2.
The RNA seq design is the following:

Sample                 experiment              siRNA                   hormonal treatment             

1                             M0                               sineg                     control

2                             M1                               sineg                     control

3                             M2                               sineg                     control

4                             M0                               sineg                     hormone

5                             M1                               sineg                     hormone

6                             M2                               sineg                     hormone

7                             M0                               siX                          control

8                             M1                               siX                          control

9                             M2                               siX                          control

10                           M0                               siX                          hormone

11                           M1                               siX                          hormone

12                           M2                               siX                          hormone


So there are two conditions (siRNA and hormonal treatment) and within each condition there are a control sample (sineg or control) and a treated sample (siX or hormone). And we realized 3 experiments (M0,M1,M2).

I would like to identify genes that respond differently to hormonal treatment in condition siX compared to the condition sineg. The design I used is the following: ~ hormonal treatment + si + hormonal treatment :si. Is it OK?

Finally I would like to take into account the experiment. In fact my experiments are paired. For example, a treatment for the experiment M0 must be compared with the control of the same experiment M0. So my question is: how do I set up the design for that?

Thanks in advance.


deseq2 • 2.4k views
ADD COMMENTlink modified 5.1 years ago by Michael Love26k • written 5.1 years ago by severine.vincent0
Answer: DESEq2 comparison with two conditions and paired experiments
gravatar for Michael Love
5.1 years ago by
Michael Love26k
United States
Michael Love26k wrote:

hi Severine,

The design to use is then:

~ experiment + hormonaltreatment + siRNA + hormonaltreatment:siRNA

This will control for the experiment effect, so taking into account the pairing of samples.

As the interaction of interest is between two factors both with only two levels, I'd recommend the following:

dds = DESeq(dds, modelMatrixType="standard")

(The standard model matrix vs expanded doesn't make a big difference, but makes the analysis simpler in this case, reducing the interaction to a single term.)

You might also consider renaming the variables to reduce your keystrokes:

siRNA with levels neg, X

hormone with levels control, treated

And don't forget to set the base level for all factors (see vignette).


ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Michael Love26k

Hi I have a similar setup of experiments (but with experiments not being paired)

I have two genotypes (geno): "A","B", Two treatments (treat): "control" "damage"

Four replicates for each genotype/treatment combination, 16 samples in total

I want to know whether the effect of "damage" compared to "control" is different between genotypes.

So I used the following design: ~geno+treat+geno:treat

and then, following the example in the ?results section of the DESeq2 vignette, I used

results <- results(dds,name="genoB.treatdamage")

However, no DEGs could be identified (all adj. p values had the same value: 0.9999928)

This is in contrast to another approach:

I first determined DEGs between genoA_control and genoB_control (comparison 1), next I determined DEGs between genoA_damage and genoB_damage (comparison 2).

Then I made a Venny, and there were 8 DEGs (adj. pvalue < E-5) in comparison 2 that were not present in comparison 1 and I also validated this by checking read coverage of these 8 DEGs in IGV.

So, I'm wondering what I should do...




ADD REPLYlink modified 12 months ago • written 12 months ago by wd30

The first procedure is a statistical test of the interaction and is the recommended test. The second is an ad-hoc procedure without FDR control on the resulting set. Sometimes intersecting FDR sets is the only option, and the resulting intersection set does not have FDR control, but here there is a statistical test that gives you the correct answer with FDR control.

ADD REPLYlink written 12 months ago by Michael Love26k

Dear Prof. Love

Thank you for your reply. I guess I'll have to perform more downstream experiments whether the DEGs of the ad-hoc procedure are meaningful.

Just to give you an idea: this is a gene that is not significantly downregulated (based on FDR) according to the recommend test (test of interaction), but based on the intersection approach this is one of the few DEG that pops up (adj. p value < e-30) in comparison 2 and not in comparison 1.


"ID"    "name"    "log2FoldChange"    "baseMean"    "lfcSE"    "stat"    "pvalue"    "padj"   
X"    "protein"    -1.88972972182758    1366.46086631548    0.880800838900554    -2.14546766802176    0.0319154738120772    0.999992751003146

"genoA_damage vs genoB_damage" ad-hoc procedure

"ID"    "name"    "log2FoldChange"    "baseMean"    "lfcSE"    "stat"    "pvalue"    "padj" 
X    protein    -0.99663284    2805.129516    0.087926543    -11.33483477    8.82E-30    9.79E-26

It is a gene that is lowly expressed in control of geno A and genoB (reads 10-20) while being highly expressed upon treatment of geno A (reads 800-900) and geno B (reads 1700-1800).




ADD REPLYlink modified 12 months ago • written 12 months ago by wd30

You are highlighting that the interaction is not significant while the main effect in the "damage" group is significant. There is nothing inconsistent here.

ADD REPLYlink written 12 months ago by Michael Love26k

Hi Dr Love

Thanks, this is really helpful and I feel that I am almost there, but I still cannot be sure so wanted to see if I had the correct set up.

My data is very similar to Severine's, it goes something like this:

see image here of sample table

I'd like to do the following comparisons, for each day:

  1. drug/nt vs. drug/target
  2. reg/nt vs drug/nt
  3. reg/target vs drug/target

Currently, my design is ~ Day + CHOW + shRNA + CHOW:shRNA, but I'm not sure this is correct. Any suggestions/corrections you might have would be greatly appreciated!!

Thank you! Mao

ADD REPLYlink modified 24 days ago • written 24 days ago by xiang.zhangm0

This is a complex design and there are many choices to work through. I'd recommend working with a statistician. I just don't have time to provide non-software related support here.

ADD REPLYlink written 24 days ago by Michael Love26k

Ok, will do. Thanks for the prompt reply and your continued support here!

ADD REPLYlink written 24 days ago by xiang.zhangm0
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