Error while using SummarizedExperiment() in R

Question

I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data:

counts_data <- exprs181517[,-1]
#Setting title col to rownames for pheno data 
rownames(pheno.data181517) <- NULL
rownames(counts_data) <- exprs181517[,1]
phenoColData <- tibble::column_to_rownames(pheno.data181517, "title")
colnames(counts_data) <- rownames(phenoColData)
#Defining the design column
designCol <- as.data.frame(phenoColData$characteristics_ch1)
rownames(designCol) <- rownames(phenoColData)

#Creating a summarized experiment
se <- SummarizedExperiment(list(counts=counts_data), colData=phenoColData)

DESeqDataSetFromMatrix(se, design ~ designCol)

but I keep getting this error:

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix':
    no method for coercing this S4 class to a vector

Answer 1

DESeqDataSetFromMatrix but a SummarizedExperiment is not a matrix. Use the function DESeqDataSet() instead and make sure the design argument is followed by a =.