Hello, I am trying to run Deseq2 on some code, but I seem to be having trouble when I run Deseq2, the error I get is "renaming the first element in assays to 'counts' Error in DESeqDataSet(SEB3, design = ~tx) : all variables in design formula must be columns in colData"

However, if I do colData(b2) the error I get is colData(b2) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'colData' for signature '"matrix"'

Does anyone have any advice? I am able to successfully make a summarized experiment with the code rounded <- data.matrix(mutate_all(as.data.frame(b2), as.integer)) SEB3 <- SummarizedExperiment(assays= SimpleList(exprs = rounded))

Start with the vignette or the workflow. You can run these examples and see whether you are providing the right information to the functions.

You should check colData(se) for a SummarizedExperiment se. This must contain the information about the samples that will be used in DE analysis.