I have a question regarding importing data into the DESeq2 pipeline using tximport.
I’m reading in salmon quant files using txiport:
tx_salmon = tximport(salmonFiles, type = "salmon", tx2gene = tx2, ignoreTxVersion=T)
After that, I make a DESeqDataSet:
dds = DESeqDataSetFromTximport(tx_salmon, colData = metadata, design = ~ condition)
Since tx_salmon$counts gives you un-normalized counts, the code above is absolutely equivalent to:
dds = DESeqDataSetFromMatrix(countData = tx_salmon$counts, colData = metadata, design = ~ condition)
Is that correct? I just wanted to confirm.