Question

RPKM value and TPM value

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3.5 years ago

anjuraas ▴ 10

Hi all I have downloaded tumor data from FireBrowse and normal data from GTEx. I want to find the differential expression between normal and tumor. But both the files are in different units. Tumor file is in RPKM values and normal file is in log2(TPM) values. Also it is not possible for me to get the raw data. What can I do in this situation? Please help me. Thanks in advance

RPKM TPM tumor normal • 1.3k views

ADD COMMENT • link updated 3.5 years ago by Bastien Hervé 5.3k • written 3.5 years ago by anjuraas ▴ 10

score 1 · Accepted Answer · 2020-10-07

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3.5 years ago

Bastien Hervé 5.3k

You can go from RPKM to TPM

https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/

If you have FPKM, you can easily compute TPM

Found this googling : RPKM to TPM conversion?

ADD COMMENT • link 3.5 years ago by Bastien Hervé 5.3k

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Hi Thanks a lot for your reply.

ADD REPLY • link 3.5 years ago by anjuraas ▴ 10

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You're welcome ! If the answer solves your question you can mark it as solved/accepted by clicking on the check icon at the left of the post. Thanks

ADD REPLY • link 3.5 years ago by Bastien Hervé 5.3k