I have 85 paired samples i.e. before and after ischemia so my question is how would I run the DEXSeq and DRIMSeq on paired samples? I’ve had a look in the relevant vignettes but cannot find any example of paired analysis.
I have a design matrix like so:
sample_id | cond | pair |
100V_post | post | 1 |
100V_pre | pre | 1 |
102V_post | post | 2 |
102V_pre | pre | 2 |
103V_post | post | 3 |
103V_pre | pre | 3 |
104V_post | post | 4 |
104V_pre | pre | 4 |
105V_post | post | 5 |
105V_pre | pre | 5 |
Dear Zoe,
One note about the rnaseqDTU workflow is that I initially made an error and included nbinomLRT() in the DEXSeq code. This should be testForDEU(). The workflow code on Bioconductor and on F1000Research has now been fixed to show testForDEU().