Dear all,

I would like to compare the expression of different genes with each other in a single biological condition (for which I have technical replicates). Transcript abundances were quantified using kallisto.

I'm a little confused with the output of tximport combined with DESeqDataSetFromTximport.

If dds is the result of the DESeqDataSetFromTximport function, I planned to use the "normalized=T" option of the counts function: dds_norm=counts(dds, normalized=T) and then to compare genes with each other based on the dds_norm counts. The objective is to select genes that are the most expressed in my biological condition.

Can you please let me know if this is correct?

Thank you for your help,

Caroline

If you want to compare expression within a sample across gene, you should use the TPMs. These can be found in txi$abundance.