I am trying to setup DEseq from RangedSummarizedExperiment, and it fails because I cannot find the column for the formula.
load("data/rse_gene.Rdata") dds <- DESeqDataSet(rse_gene, design = ~some_condition) # some_condition is a random name, it is not in the data.
It fails with:
Error in DESeqDataSet(rse_gene, design = ~some_condition) : all variables in design formula must be columns in colData
With a plain counts file, I add this column after loading to the data.frame and everything works. Do I need to add some_condition to the RangedSummarizedExperiment object?
I have tried this with 3 different rse_gene.Rdata files from recount2 - all have the same issue.