Hi everyone,

I am new in bioinformatics and when I try to use DESeq2 for my counts and further downstream analysis, I am faced with this problem.

dds <- DESeqDataSetFromMatrix(countData = count_matrix, colData = NULL, tidy = TRUE) Error in rownames<-(tmp, value = colnames(countData)) : attempt to set 'rownames' on an object with no dimensions

When I check the type of my count_matrix it is all integer (lapply(count_matrix, class). I don't know whats wrong. I would appreciate if someone helps. Thank you.

I think you need to provide a DataFrame or a data.frame with at least one column as the colData argument. From the DESeqDataSetFromMatrix help page:

countData <- matrix(1:100,ncol=4)
condition <- factor(c("A","A","B","B"))
dds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), ~ condition)

Also, can you clarify what your count_matrix actually looks like? (Perhaps you can show the output of the class(count_matrix) and head(count_matrix) commands?) Does it have column names (and does the first column correspond to your feature identifiers, given that you set tidy=TRUE)?