HI

I am using the tximport module to process the output of Salmon. Then I am using the vst(dds) to normalise the data. I understand that the assay for dds is count. How can I process the abundance(TPM) using the vst so that my TPM data is normalised. 

My R code looks:

txi <- tximport(files, type="salmon", tx2gene=tx2gene, ignoreTxVersion=TRUE,dropInfReps=TRUE)
sampleTable <- data.frame(condition =samples$condition,time=factor(samples$time))
rownames(sampleTable) <- colnames(txi$counts)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~condition+time)

vsd <- vst(dds) 

The VST is only designed for counts. We recommend using variance stabilized, transformed counts for downstream applications like visualization, distances, clustering or classification/prediction methods that benefit from homoskedastic data.

TPM is useful for comparing abundance across transcripts or genes. It should be proportional to the true abundance of RNA molecules.