Dear Bioconductor community,
I'm analyzing RNA-seq data with limma-voom.
This experiment involves 6 subjects, including 3 animals who dead after infection by a virus and 3 animal who survive.
From each subject, blood were collacted before any treatment (D0) and at different time points after infection (as animal are not dying the same day, we have missing time point for some animals). There is a single time point (Day 3) for which we have data in dead and alive animals. So, I would like to identify genes that respond differently at Day3 in Alive relative to the Dead animals.
The correlation is very low (0.18). Should I performed the analysis without duplicateCorrelation ?
What is the best way to analyse such data ?
Thanks in advance for your help