Hi,

I am using DESeq2 to form a contrast between three different conditions as below:

shortname    condition
Center1    center
Center2    center
Center3    center
Edge1    edge
Edge2    edge
Edge3    edge
Swim1    swim
Swim2    swim
Swim3    swim

My design is as follows

coldata = with(samples,data.frame(shortname = I(shortname), condition = condition))

dds <- DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~ condition)

dds$condition = relevel(dds$condition, "swim")

dds <- DESeq(dds)

resultsNames(dds)

This is giving this output

[1] "Intercept"                "condition_center_vs_swim" "condition_edge_vs_swim" 

However, I want the following as output

[1] "Intercept"                "condition_center" "condition_edge"  "condition_swim" 

I want to generate contrasts on my own and then find the DE genes in my contrast.

Is there something wrong in my code. Please help...