I'm having difficulties to set up the best design for my experiment. I have 9 different groups (different metals) and a time-course (1,3,6 and 9 months). One of those metals will be my control, and I'm trying to see what miRNAs are changing among metals in each time-point and also if there is a difference among the time point. All samples are independent.
I have so far:
dds<-DESeqDataSetFromMatrix(countData= countData,colData= colData,design= ~ Condition + Time) dds<-DESeq(dds, test = "LRT", full = ~ Condition + Time, reduced = ~Time) head(colData) Names Condition Time Ta-3-1 Ta3 Day3 Ta-3-2 Ta3 Day3 Ta-3-3 Ta3 Day3 W-3-1 W3 Day3 W-3-2 W3 Day3 W-3-3 W3 Day3 Ni-3-1 Ni3 Day3 Ni-3-2 Ni3 Day3 Ni-3-3 Ni3 Day3 Co-3-1 Co3 Day3 Co-3-2 Co3 Day3 Co-3-3 Co3 Day3 Fe-3-1 Fe3 Day3 Fe-3-2 Fe3 Day3 Fe-3-3 Fe3 Day3 Cu-3-1 Cu3 Day3 . . . Ta-1-1 Ta1 Day1 Ta-1-2 Ta1 Day1 Ta-1-3 Ta1 Day1 Ta-1-4 Ta1 Day1 Ta-1-5 Ta1 Day1 dds<-DESeq(dds, test = "LRT", full = ~ Condition + Time, reduced = ~Time) resultsNames(dds)  "Intercept" "Condition_Al_vs_Ta" "Condition_Co_vs_Ta" "Condition_Cu_vs_Ta" "Condition_DU_vs_Ta"  "Condition_Fe_vs_Ta" "Condition_Ni_vs_Ta" "Condition_Pb_vs_Ta" "Condition_W_vs_Ta" "Time_Day12_vs_Day1"  "Time_Day3_vs_Day1" "Time_Day6_vs_Day1"
I understand that the LRT is doing the test in all the conditions. However, I want to be able to compare the metals (e.g. Al vs Ta). But I want to do that for 1, 3, 6 and 12 months. Since is not on my Names() I don't know how to proceed.
Thanks in advance