Hi, I have a question regarding the normalization process when using tximport for processing Salmon output. Specifically, my workflow involves setting the countsFromAbundance parameter to "lengthScaledTPM" for collating read counts.
My question pertains to the necessity and method of library size normalization after obtaining the txi$counts from tximport. Considering the adjustment made by using "lengthScaledTPM", is further normalization for library size required when using txi$counts for downstream analysis? Additionally, if library size normalization is necessary, does this imply that the output from txi$counts is effectively in Reads Per Kilobase (RPK) format?
I appreciate any insights or recommendations on whether library size normalization is needed in this context and the correct interpretation of the txi$counts output under these conditions.
SG
txi <- tximport(files,
type = "salmon",
tx2gene = tx2gene,
countsFromAbundance = "lengthScaledTPM")
See also this related question:
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?