I am attempting to compare the following samples in DESEQ2 that follow and experimental design of:
condition celltype Ctrl A Ctrl B Ctrl C Ctrl D CYTO A CYTO B CYTO C CYTO D
(Replicates left out for simplicity sake)
The researcher has requested I compare cell types to each other (A vs. B, A vs. C, A vs. D, B vs. C etc). I know how to compare Cell type A vs Cell type B for Control and CYTO, separately. I did this by merging condition and celltype into a new column called group, and called
results(dds, contrast=c("group", "ACtrl", "BCtrl"))
However I would like to compare A vs. B across condition. Reading online, I have found this might be what I need to test genes which respond differently to cell type across condition:
design = ~ condition + celltype + condition:celltype >resultsNames: # "C" is the reference  "Intercept" "condition_CYTO_vs_Ctrl" "celltype_A_vs_C"  "celltype_B_vs_C" "celltype_D_vs_C" "conditionCYTO.celltypeA"  "conditionCYTO.celltypeB" "conditionCYTO.celltypeD"
Assuming this is correct, my confusion lies in calling the correct comparison in results. Do i need to use "name", "contrast", "list", "contrast=list" ?
Thank you in advance