The vignette of GOseq details in section 6.8 how to correct for total read
count bias (per gene). The code used to calculate total read count bias
incorporates raw coverage counts instead of normalized counts.

 When there are dramatic changes in library size, is it more appropriate to
use the normalized counts instead? Would taking the log2 transformation of
the total read counts also help improve the spline fitting of the
probability weighting function (PWF)?

Thank you,
Chris Conley
Research Assistant
UC Davis Genome Center

	[[alternative HTML version deleted]]

