How to describe LRT test condition for time series RNA-seq data of 2 varieties
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Last seen 2.7 years ago

I have RNA-seq data of two varieties under control and treated condition derived at different time points. I want to extract DEGs between variety1 and variety2 due to the treated vs. control condition at each time point. As per my understanding, LRT test will give the DEGs but I am unable to design the condition for LRT test. My data is as follows:

Variety 1

Control Treated 1stday 1stday 5thday 5thday 10thday 10thday

Variety 2

Control Treated 1stday 1stday 5thday 5thday 10thday 10thday

1.) Will the following design will provide me the desired results? full = ~ (Variety1/Variety2)+ (Treated/Control)day1 + variety:treatedday1) reduced = ~ (Variety1/Variety2)+ (Treated/Control)day1

2.) How can I create variables in colData such as factor variable for the time points and condition (control/trated) and for variety(1,2) and how can I describe the condition in dds <- DESeq command?

deseq2 LRT RNAseq condition • 403 views
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Last seen 4 days ago
United States

Unfortunately, I don't have sufficient time at this point to offer statistical design help on the support site, I have to limit myself to software related questions only. I'd recommend working with a local statistician on (1) and (2).


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