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Old 08-13-2014, 02:47 PM   #1
NikTuzov
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Default A question about TPM normalization

Hello:

Please tell me if I got it right. In the attached paper, the average read length, rl, is not necessary to know for computing TPM. It is sample-specific, but not gene-specific, and that is why it cancels out in the TPM formula and also in the formula that describes the relationship between TPM and RPKM.

Thanks,
Nik
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File Type: pdf Wagner et al 2012.pdf (228.0 KB, 34 views)
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Old 08-16-2014, 07:18 AM   #2
gpwagner
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Default readlength in TPM calculation

Dear Nick,

Yes the read length is canceling from the equation. The reason I left it in the equation is for conceptual clarity, to indicate what TPM is measuring. But yes, for calculating tpm you can forget rl.

Sincerely,
Gunter
(Gunter Wagner, Yale U)
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Old 08-18-2014, 11:58 AM   #3
NikTuzov
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Default

Thanks a lot.

Nik
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