Deseq2 colData for single condition

Question

[Petesview]

Hi,

I have an RNA-seq dataset that I wish to compare between treated vs control following the DESeq2 vignette. I have no other meta information about this dataset, therefore my colData only contains a single column describing which sample is treated and which is control. My design matrix is (design = ~ condition).

When I perform DEseq2 on this object, the results look fine, but when I try to use the resultsName function on the dds object, nothing is returned (character 0). May I ask if I am doing this correctly?

[Marco Pannone]

You first need to run

dds$condition <- relevel(dds$condition, ref = "control")

[Petesview]

Hi Marco, thanks for the reply. I have given it a try, using both the relevel and factor functions as suggested by the vignette, but still gives me character0 for resultsName function