Hi,

I have a dataset with a complex design : 2 years, each year 4 varieties, each variety 5 time points. I'm using LRT test for DE analysis. The results names for Year and Time_Point are ok, but for Variety there is a reference base while I want compare them pairwise with LRT test, is there any solution? Thank you in advance

dds<- DESeqDataSetFromMatrix( countData, colData, design = ~ Year + Time_Point + Variety)

ddsLRT <- DESeq(dds, test="LRT", reduced = ~ Year + Time_Point )

resultsNames(ddsLRT)

[1] "Intercept" "Year_y2013_vs_y2010" "Time_Point_T2_vs_T1"
[4] "Time_Point_T3_vs_T1" "Time_Point_T4_vs_T1" "Time_Point_T5_vs_T1"
[7] "Variety_Iso8s_vs_Iso11w" "Variety_Manitou_vs_Iso11w" "Variety_Norstar_vs_Iso11w"

We don't offer pairwise contrasts for an LRT, but you can use a Wald test with the contrast argument.