Hello! I loaded my gene(/transcript) count matrix and labels into DESeq2:
> countData <- as.matrix(read.csv(file.choose(), row.names = "gene_id")) > colData <- read.table(text = readLines(file.choose(), warn = FALSE), header = TRUE, sep = "," )
But when I check that all sample IDs in colData are also in CountData and match their orders, I obtain the following:
> all(rownames(colData) %in% colnames(countData))  FALSE
It then checked to see how my gene_count_matrix.csv looks like and the column has MSTRG as the gene ID and it does not match the ID names found in phenotype_data.
I was wondering how do I make them both match so that I am able to generate a DESeqDataSet? My phenotype_data looks just like the data found in the nature paper
and I followed exactly the protocol for Using StringTie with DESeq2.