Using RPKM to compare gene expression between samples
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7 weeks ago
kz • 0

Hi all, wondering if normalisation using log2(rpkm + 1) is suitable for comparing gene counts between samples and groups. I see this quite often in pubs, e.g.:

Screen-Shot-2021-04-26-at-4-42-52-pm

But I came across this, which says RPKM is for "gene count comparisons between genes within a sample; NOT for between sample comparisons or DE analysis"

Thanks!

rnaseq normalization rpkm • 128 views
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Entering edit mode
7 weeks ago
dsull ★ 1.9k

The pubs that do things like that are doing things incorrectly. If you're comparing between samples, there are many programs written for that purpose (e.g. deseq2, sleuth, edgeR, etc.)

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