Question: DESeq2 on two groups
0
gravatar for pokharel.kisun
16 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 • 316 views
ADD COMMENTlink modified 15 months ago by Michael Love26k • written 16 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 16 months ago by Michael Love26k

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 15 months ago by pokharel.kisun0
Answer: DESeq2 on two groups
2
gravatar for Michael Love
15 months ago by
Michael Love26k
United States
Michael Love26k 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 15 months ago by Michael Love26k

Thanks for the suggestion. 

ADD REPLYlink modified 15 months ago • written 15 months ago by pokharel.kisun0
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