Asked this question on Twitter and thought I would share answers here via Storify. I am putting it below the fold to allow people to avoid the Storify embed if they want to.
//storify.com/phylogenomics/correcting-for-rrna-copy-in-qpcr-data.js[View the story “Correcting for rRNA copy # in qPCR data” on Storify]
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Jonathan Eisen's Lab 