Entering edit mode
Background: Following DESeq2 tutorials, I'm importing Kallisto abundance.tsv files using tximport, creating a DESeq2 dataset, and rlog transforming the data for downstream figure generation. Question: What column of Kallisto abundance.tsv is transformed using "rlog(dds)"? In other words, is DESeq2 "rlog" acting on Transcript per million (tpm) or raw abundance values (est_counts) from the Kallisto abundance.tsv files?
txi<- tximport(files, type="kallisto", tx2gene = tx2gene)
dds <-DESeqDataSetFromTximport(txi, colData=samples, design = ~Batch + Condition)
dds <- DESeq(dds)
rld <- rlog(dds, blind=FALSE)
#not relevant to the question, simply showing an example of using rlog transformed data in figures
plotPCA(rld, intgroup=c("Condition", "Batch"))
Abundance. If you look at the counts in dds, they should match abundance, not TPM (unless there is a slight shift due to the transcript-length offset value)