Question

DESeq2 on two groups

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pokharel.kisun • 0

@pokharelkisun-9612

Last seen 6.3 years ago

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 • 1.2k views

ADD COMMENT • link updated 6.3 years ago by Michael Love 43k • written 6.3 years ago by pokharel.kisun • 0

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

ADD REPLY • link 6.3 years ago Michael Love 43k

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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 REPLY • link 6.3 years ago pokharel.kisun • 0

score 2 · Accepted Answer · 2018-08-14

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Michael Love 43k

@mikelove

Last seen 2 days ago

United States

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.