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...