In Salmon result, there is a TPM column but it is from transcript level. I want to use tximport library to get TPM values for gene level.
per_gene <- tximport(salmon_file_list, type = "salmon", tx2gene = trs2gene)
I use that code and I get this:
names(per_gene)  "abundance" "counts" "length" "countsFromAbundance"
There are no TPM but I read there is a parameter countsFromAbundance with scaledTPM and lengthScaledTPM.
Is this parameter can be used to get TPM? Which values (scaledTPM or lengthScaledTPM) are better if I want to compare TPM accross different experiment (i.e independent RNA-seq experiment but same cll type)? How can I get this from the result? is per_gene["countsFromAbundance"] store the values?