Question: DESeq2 on two groups
0
gravatar for pokharel.kisun
5 months ago by
pokharel.kisun0 wrote:

Hi,

I just wanted an honest opinion on whether to include two groups together or analyse separately in DESeq2 (please see the pca plot using the link below). I am inclined towards analysing separately, but I want to hear from the readers.

Here, the two groups represent two tissues and within each tissue there are three sub-groups (three breeds)

 

https://drive.google.com/file/d/1n8Lac8ywF4R3MOItRi-V6TVGretrKvg5/view?usp=sharing

Thank you!

Kisun

deseq2 group • 170 views
ADD COMMENTlink modified 5 months ago by Michael Love21k • written 5 months ago by pokharel.kisun0

You need to post more information. How can you perform differential analysis with less than two groups?

ADD REPLYlink written 5 months ago by Michael Love21k

Hi Mike, sorry for incomplete post. The study consist two breeds and their F1 (i.e 3 breed groups) and two tissues. The two groups you can see in the PCA is for two tissues. One tissue (E) is more heteregenous than the other (C). Within E, there is high within-group variability. I have updated the post but I will also upload another PCA.

ADD REPLYlink written 5 months ago by pokharel.kisun0
Answer: DESeq2 on two groups
2
gravatar for Michael Love
5 months ago by
Michael Love21k
United States
Michael Love21k wrote:

Is there additionally batch information? It looks like the right group is split 3/3, 3/3/ and 2/4 by something other than what you've got being used to color now.

If you suspect batches, you could use sva or RUVSeq to identify them. See the last section of our workflow.

If not, then yes, I'd recommend splitting into a C dataset and an E dataset to perform DE analysis separately, as they will have very different estimates of variability.

ADD COMMENTlink written 5 months ago by Michael Love21k

Thanks for the suggestion. 

ADD REPLYlink modified 5 months ago • written 5 months ago by pokharel.kisun0
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