Hi, I am analyzing RNA-seq data with four factors: Condition (WT and MT), CellLine (2 cell lines in each condition), Replicate (3 replicates in each cell line) and library (paired pull-down and control for a replicate): total 2*2*3*2=24 samples (Table is the below). I would like to find the difference of pull-down/control (by paired) between the two conditions: WT and MT controlling CellLines. The issue is that cell lines are nested in conditions and replicates are nested in cell lines. How can I design the formula for DESeq2? Based on the DESeq vignette, I created the variable to recode cell line with two levels called "1" and "2" as the last column in the table and tried two designs: (1) Condition + Condition:CellLineSuppressed + Condition:CellLineSuppressed:Replicate + Condition:Library (2) Condition + Condition:CellLineSuppressed + Condition:Replicate + Condition:Library. Please let me know your advise !! Also, note that I didn't include a single "library" term in the design. Is it okay?