Hi,

I am interested in comparing the expression of genes within the same sample and ranked them from the most expressed to the least expressed. I cannot use counts nor normalized counts because they do not take into account the gene lengths. Which measure would you suggest I use? Does DESeq2 provides a function to transform raw counts into such format?

You can transform your raw counts to FPKM or TPM (recommend) for such within-sample comparsion, as these two normalization both takes gene length into consideration.