Hello guys!

I've been trying to run a DESeq on my RNA seq data, however, when I read in my data and try to run a "DESeqDataSetFromMatrix" the following error pops up. I could really use some help.

#read in counts data
counts_data <- read.csv('forDESeq2.csv')

#for some reason I have gene name duplicates, this eliminates it
rownames(counts_data) <- make.names(counts_data$external_gene_name, unique = TRUE)
counts_data <- counts_data[,-1]
colData <- read.csv('colData.csv', header = TRUE, sep = ",", col.names = 'groups')

#to check whether the rows and columns are the same
all(colnames(counts_data) %in% rownames(colData))
all(colnames(counts_data) == rownames(colData))

#to check whether there is a negative value
any(counts_data < 0)

dds <- DESeqDataSetFromMatrix(countData = counts_data,
                              colData = colData,
                              design = ~ groups)

Any assistance is appreciated!

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your counts_data indeed only contains counts, do:

mode(counts_data) <- "numeric"