Repeated measures RNAseq analysis (edgeR or limma-voom)
Entering edit mode
jackgisby • 0
Last seen 3.0 years ago
United Kingdom

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 limma variancePartition • 1.3k views
Entering edit mode
Last seen 4 hours ago
WEHI, Melbourne, Australia

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


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