Hello!

I am performing a transcript level differential expression analysis. For the same, I have quantified my samples using salmon and am using tximport as an offset before DESeq2. I wanted to know whether passing scaledTPM values is recommended to DESeqDataSetFromTximport? I am attaching my code below. Any help is appreciated. Thanks!!

txi <- tximport(files, type= "salmon", txOut=TRUE, countsFromAbundance="scaledTPM")

sampleTable <- data.frame(condition = factor(samples$condition))
rownames(sampleTable) <- colnames(txi$counts)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition)

Either is fine (countsFromAbundance (cFA) = "no" or the other options which scale TPM to act like counts):

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Downstream_DGE_in_Bioconductor

I personally recommend cFA = "no" when using DESeq2 or edgeR.