I loaded a set of samples into DESeq2 with one factor that has three levels. There is a single condition I called "Type" with three levels A, B, C.
This is what I did:
I can use contrasts to run any of the pairwise comparisons. What if I want to get the differences between all three factors? Is that possible? What is the proper approach for that?
This is what I did:
Code:
> ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design = ~ Type) > dds <- DESeq(ddsHTSeq, betaPrior=FALSE) > resultsNames(dds) [1] "Intercept" "Type_B_vs_A" "Type_C_vs_A"
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