Hi, I would to use DESeq2 to process three bulk RNASeq paired samples but I am trying to figure out what is the valid model to use here. I used tximport to import Kallisto's transcript-level abundance estimates at gene level to use with deseq2.
In the paired samples, the treatment is overxperssion of gene A. Sample information is as follows:
condition patient_id BT12CONT Control BT1 BT12OE OverExp BT1 BT53CONT Control BT53 BT53OE OverExp BT53 GBM5CONT Control GBM5 GBM5OE OverExp GBM5
I am interested in looking at the condition effect while accounting for sample pairs so I thought a model like the following would be enough:
> ~ condition + patient_id
The PCA for these samples shows that the samples separate by patient_id
Is this simple model to look at condition/treatment effect enough?