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Old 06-16-2015, 11:20 AM   #2
swbarnes2
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Location: San Diego

Join Date: May 2008
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RPKM is counts, but corrected for differences in gene length between genes, and differences in overall read numbers between samples. You certainly do need to correct for the fact that not all samples get the same # of reads; you don't want one sample ranking as #1 for every gene because it got twice as many reads as everything else. Correcting for gene length is likely not going to matter since you are ranking.
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