Hi all,

I have an experiment with serial sampling that I want to model (for e.g. presence of disease, disease severity). I want to know what the best way to go about this would be when doing differential expression analyses. My questions are:

1. Can I handle repeated measurements using edgeR? My understanding is no based on previous posts (e.g. Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis ) but I wanted to check this information was up to date and that limma/voom is the best option for this.
2. Is there a method that will allow me to use more complex random effect specifications? I understand that limma-voom's duplicateCorrelation and the dream functions from variancePartition will only allow for random intercepts and not random slopes.

edgeR does not support random effects. We don't have any concrete plans to change that.