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It's not possible to get raw counts, so I'd avoid methods that strictly require those.RPKs adjust for gene length but not sequencing depth, so you'll want to manage the latter in SOME way. One option is to normalize the RPKs to relative abundance or CPM units (e.g. via the renorm_table script).Thanks,Eric
On Fri, Dec 20, 2019 at 9:18 AM Minjae Kim <minja...@gmail.com> wrote:
--Hello,Since the metagenomic data is compositional data, I just wonder if it is okay to apply LefSE and other statistical comparisons with RPK value from humann2.or is it better if we can use raw counts and normalize with metagenomeseq, DESeq2, or EdgeR? (is it possible to have raw counts?)What is the best recommendation with humann2 output for the comparisons?Thanks
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