hello there, I am not fully sure what I am doing here. Basically, I have always known that when using tsv files, there should not be any inferential replicates considered. But now, in the latest version of tximport, I guess something has changed?

> txi.kallisto.tsv <- tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreTxVersion = TRUE)


 Note: importing `abundance.h5` is typically faster than `abundance.tsv`
 reading in files with read.delim (install 'readr' package for speed up)
 1 2 3 4 5 6 
 transcripts missing from tx2gene: 22002
 summarizing abundance
 summarizing counts
 summarizing length
 summarizing inferential replicates

I would like to ask if, in this way, inferential replicates are automatically taken into account for the downstream analysis or it is just a new warning message that can also be ignored, because:

> rownames(sampleTable) <- colnames(txi.kallisto.tsv$counts)
> dds <- DESeqDataSetFromTximport(txi.kallisto.tsv, sampleTable, ~condition)
using counts and average transcript lengths from tximport
> dds <- DESeq(dds)
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

thanks

This is a few versions back I think.

tximport imports inferential replicates if they are present, and you can prevent this with dropInfReps=TRUE. By the way, those are messages above, not warnings.

The inferential replicates are not used by DESeq2.