I imported a set of
salmon quantifications into R with
tximport default settings and exactly used the code on the manual page for tximport to prepare data for use with
edgeR. The result is a
DGElist with the offsets for the downstream DGE analysis.
y$samples) does not contain the
lib.size factors (they are all 1) for obtaining TMM-normalized counts via
Therefore, the question is how to feed normalization factors into
y$samples$norm.factors while still using the information from
One can of course run
calcNormFactors(y) manually but then the length offsets from
tximport are lost. Is there a recommended approach?