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