The Downstream DGE in Bioconductor section in the tximport vignette has two Notes in it and nothing else, and the way things are explained there is confusing.

Which of the two code snippets below is the correct approach for importing (and subsequently passing on to DESeq2) expression levels quantified using Salmon with the transcript-gene relationship given by a two column data.frame named tx2gene?

(1):

txi <- tximport::tximport(files = flist, type = "salmon", tx2gene = tx2gene, countsFromAbundance="lengthScaledTPM")
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~cond)

(2):

txi <- tximport::tximport(files = flist, type = "salmon", tx2gene = tx2gene)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~cond)