I have a multi-factor design RNA-seq experiment I am analyzing with DESeq2. I am having trouble with the design due to "model matrix not full rank". I have been trying to work my way through the advice from the vignette and previous posts on this issue...
Here is my colData:
Essentially, I am interested in: 1) what are the DE genes between infected and control? and 2) do the DE genes found differ depending on condition?
"Tank" denotes the enclosure the animals were sampled from, and needs to be controlled for in analyses if possible. Trying to follow previous posts, I tried to nest tank within treatment (hence the tank.nested column above). However, I realise that tank A&B are still only within high, C&D only within low etc. so have not solved the issue.
Could anyone suggest how to set up my colData and/or design to resolve the error of model matrix not full rank? And which results() and contrast=list should allow me to get at the comparisons I am trying to make.
I am getting myself very confused - I am waiting on a meeting with a local statistician to help me work through it. But would really appreciated some help in the meantime to try to get my head around it! Many thanks in advance.