Hi! I am running a DESeq2 analysis in where I have 24 groups (A-W). In order to get the "unique" DEG from each group, I would like to compare a specific group against all the rest (e.g. A vs B-W). I tried to use the contrast tools but I kept getting this error.

dds <-DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ group_time) res <- results(dds, contrast = list (c("A"), c("B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X")), listValues = c(1,-1/23) )

Error in checkContrast(contrast, resNames) : all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)'

Which are: "group_time_B_vs_A" "group_time_C_vs_A" "group_time_D_vs_A" "group_time_E_vs_A" "group_time_F_vs_A" [7] "group_time_G_vs_A" "group_time_H_vs_A" "group_time_I_vs_A" "group_time_J_vs_A" "group_time_K_vs_A" "group_time_L_vs_A" [13] "group_time_M_vs_A" "group_time_N_vs_A" "group_time_O_vs_A" "group_time_P_vs_A" "group_time_Q_vs_A" "group_time_R_vs_A" [19] "group_time_S_vs_A" "group_time_T_vs_A" "group_time_U_vs_A" "group_time_V_vs_A" "group_time_W_vs_A" "group_time_X_vs_A"

And then I don't know how to proceed. Thank you in advance for your help!

Another way you could do this is to make a new column in colData, with only two values, "A" and "notA". It will be slightly different from the list way, but it's probably easier to handle.