Hello, I am interested in doing a pairwise condition with DEXSeq, I have read your earlier answer here: C: Pairwise comparasion for multiple conditions using DEXSeq, but I am still confused as to how to implement it. How would I subset the DEXSeqDataSet? I have 2 conditions, 3 replicates each, and 3 stages. Overall, 18 different samples. My data set looks like this:

         condition stage

GFP_18_1       GFP    18

GFP_18_2       GFP    18

GFP_18_3       GFP    18

GFP_28_1       GFP    28

GFP_28_2       GFP    28

GFP_28_3       GFP    28

GFP_38_1       GFP    38

GFP_38_2       GFP    38

GFP_38_3       GFP    38

ICD_18_1       ICD    18

ICD_18_2       ICD    18

ICD_18_3       ICD    18

ICD_28_1       ICD    28

ICD_28_2       ICD    28

ICD_28_3       ICD    28

ICD_38_1       ICD    38

ICD_38_2       ICD    38

ICD_38_3       ICD    38

I would like to compare GFP 18 vs ICD 18 (overall not individual replicates), GFP 28 vs ICD 28, etc. How would I subset this and what would be my design matrix, currently I am using ~sample + exon + stage:exon + condition:exon + stage:condition:exon. I have also used ~sample + exon + stage:exon + condition:exon, but I am still trying to figure out the differences between the comparisons. I also would like to know what fitExptoVar variable would be best for my experiment. Thank you!