I'm performing differential gene expression analysis using DESeq2, and my input files are Salmon quantification files at the gene level (.quant.genes.sf). I would like to clarify the appropriate use of the tximport parameters: countsFromAbundance txOut Given that the input files are already summarized at the gene level, what are the recommended settings for these options to ensure compatibility with DESeq2? Any guidance would be greatly appreciated.

> txi <- tximport(files,
+                 type = "salmon",
+                 txOut = TRUE,                    # already gene-level
+                 ignoreTxVersion = TRUE,
+                 countsFromAbundance = "lengthScaledTPM")  # or "no"
# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 
sessionInfo( )

The tx in the name stands for transcript. Gene level needs no tximport. You could simply use the standard output from salmon and do what the tximport vignette suggests.