How to use a design matrix with two control levels in DESeq2

Question

[Pac314]

Hi I am trying to run DESeq2 using a design matrix with two control levels (cont_A and cont_B). I am interested in the following contrasts:

1. grp_A1 vs cont_A
2. grp_A2 vs cont_A
3. grp_B1 vs cont_B
4. grp_B2 vs cont_B
5. grp_B3 vs cont_B

My output for dput on colData:

structure(list(group = structure(c(1L, 1L, 1L, 1L, 3L, 3L, 3L, 
3L, 5L, 5L, 5L, 5L, 2L, 2L, 2L, 2L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 
5L, 6L, 6L, 6L, 6L), levels = c("cont_A", "cont_B", "grp_A1", 
"grp_B1", "grp_B2", "grp_B3"), class = "factor"), replicate = structure(c(1L, 
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L), levels = c("rep1", 
"rep2", "rep3", "rep4"), class = "factor")), class = "data.frame", row.names = c("S1", 
"S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", 
"S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", 
"S21", "S22", "S23", "S24", "S25", "S26", "S27", "S28"))

dds <- DESeqDataSetFromTximport(txi, colData=colData, 
                                design=~replicate+group)
dds

# extracting results with contrast
res <- results(dds, contrast=c('group', 'grp_B1', 'cont_B')
# shrinking lfc
res <- lfcshrink(dds, coef='group_grp_B1_vs_cont_B', res=res, type='apeglm')

When I shrink the LFC with apeglm I get the following error:

Error in lfcShrink(dds, coef = "group_grp_B1_vs_cont_B", type = "apeglm") : 
  coef %in% resultsNamesDDS is not TRUE

The resultsNames() output:

> resultsNames(dds)
 [1] "Intercept"              "replicate_rep2_vs_rep1" "replicate_rep3_vs_rep1" "replicate_rep4_vs_rep1"
 [5] "group_grp_B1_vs_cont_A"    "group_grp_B2_vs_cont_A"    "group_grp_B3_vs_cont_A"    "group_cont_B_vs_cont_A"   
 [9] "group_grp_A1_vs_cont_A"     "group_grp_A2_vs_cont_A"