Running more than 2 conditions in DeSeq2

Stephanie Lj Tan

• July 16, 2021 12:13

Hi there,

I am trying to set up an expression analysis between 3 different sample strains from my RNA-seq experiment that were also taken at 3 different timepoints. I have 3 biological replicates for each, so 27 samples in total. Currently, I can see that I can only run DeSeq2 on 2 conditions only - is there a way to do more than 2 and how? 

Thanks

Stephanie

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  Hilary Miller

  • July 18, 2021 23:51

  Sorry, its not possible to do 3 sample conditions in RNAseq analysis in Geneious.  Only 2 sample with replicates is currently possible.  

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