Differential expression analysis in DESeq2 for an experiment with multiple variable
1
0
Entering edit mode
4.4 years ago
Mozart ▴ 330

Dear all, I am approaching a kinda new experiment and wondering what is the best way to construct my design, to plug into DESeq2, in order to best address my question of interest.

  • First we have, 10 replicates of mouse cells from tissue X taken at two different steps of their life cycle (let's say cycle A and cycle B). These cells were taken from lab 1. Samples were paired-end sequenced.
  • Second, 10 replicates of mouse cells from tissue Y taken at two different steps of their life cycle (again, cycle A and cycle B). These cells were taken from lab 2. Samples were single-end sequenced.

All of these samples are balanced and/or paired (?), meaning that each biological replicate is taken from the same mouse each time. For example, from mouse 1 were extracted cells at both cycle A and cycle B.

So, same cell types at two separate conditions but extracted from two different labs (in two different parts of the globe). I am relatively new to this kind of design formula. But, what I want to do is:

  • First, find differentially expressed genes within each lab (i.e. A vs B from lab 1; A vs B from lab 2)
  • Second, try to compare everything across each lab in all the possible combinations but also caring of the different above mentioned variables.

To sum up we have a four different variables

  1. cycle

  2. tissue

  3. replicate

  4. lab

Therefore I would suggest a design matrix like the following one: ~ tissue + tissue:cycle + replicate + batch + cycle

I am just throwing an idea, I am not 100% sure.

Thanks in advance

deseq2 RNA-Seq • 949 views
ADD COMMENT

Login before adding your answer.

Traffic: 1292 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6