Hi Mike-

Thanks for the clarification below - I don’t know how I missed that.


​No, it does account for sequencing. We say explicitly in the vignette and man pages that the rlog is better for accounting for size factors differences than VST. Also the formulae provided in the vignette and man pages makes this clear:

rlog is defined as log2(q_ij)​
​
E(K_ij​) = mu_ij = s_j q_ij

in words, the expected count for gene i, sample j is represented by mu_ij, which is the produce of a size factor, s_j, which accounts for sequencing depth and q_ij.  So q_ij therefore is the part leftover after accounting for sequencing depth.


Thanks,
Kristina


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Kristina Fontanez, Postdoctoral Fellow
fontanez@mit.edu<mailto:fontanez@mit.edu>
Massachusetts Institute of Technology
Department of Civil and Environmental Engineering
48-120E
15 Vassar Street
Cambridge, MA 02139


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