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Difference between CPM and TPM and which one for downstream analysis?
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+ Biochemistry
+ Rna-seq
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Keith Allpress
Difference between CPM and TPM and which one for downstream analysis?
You can find the various equations in this oft-cited blog post from Harold Pimentel. CPM is basically depth-normalized counts, whereas TPM is length-normalized (and then normalized by the length-normalized values of the other genes).
If one has to choose between those two choices one typically chooses TPM for most things, since generally the length normalization is handy. Realistically, you probably want log(TPM) since otherwise noise in your most highly expressed genes dominates over small expression signals.
You can find the various equations in this oft-cited blog post from Harold Pimentel. CPM is basically depth-normalized counts, whereas TPM is length-normalized (and then normalized by the length-normalized values of the other genes).
If one has to choose between those two choices one typically chooses TPM for most things, since generally the length normalization is handy. Realistically, you probably want log(TPM) since otherwise noise in your most highly expressed genes dominates over small expression signals.
@novicebioinforesearcher No, transcript/gene length, which correlates (somewhat) with counts and therefore will tend to drive clustering unless handled in a reasonable way.More
You can find the various equations in this oft-cited blog post from Harold Pimentel. CPM is basically depth-normalized counts, whereas TPM is length-normalized (and then normalized by the length-normalized values of the other genes).
If one has to choose between those two choices one typically chooses TPM for most things, since generally the length normalization is handy. Realistically, you probably want
log(TPM)since otherwise noise in your most highly expressed genes dominates over small expression signals.You can find the various equations in this oft-cited blog post from Harold Pimentel. CPM is basically depth-normalized counts, whereas TPM is length-normalized (and then normalized by the length-normalized values of the other genes).
If one has to choose between those two choices one typically chooses TPM for most things, since generally the length normalization is handy. Realistically, you probably want
log(TPM)since otherwise noise in your most highly expressed genes dominates over small expression signals.More
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