Conversion from FPKM,RPKM to tpm
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Sandhiya • 0
@8bdd529f
Last seen 3.1 years ago
United States

Hi all,

I'm trying to collect the datasets from public datasets from GEO. I found some data in fpkm and some in rpkm,tpm. My goal is to feed these data into a machine learning model, but my question is "ALL THESE DATA SHOULD BE IN A COMMON FORMAT "; to do this what's the best solution?

I have two questions:

1) To have a common unit, I should convert these data to tpm ie., fpkm,rpkm to tpm; so that all values are in same format In this case how can I do this conversion?

2) If I decide to use DESeq2 to normalize; then is it right to feed all these different file formats into DESeq2 and uniformly have deseq2 normalized values?

Please help me with this?

Thanks!

DESEQ2 fpkm rpkm tpm • 5.0k views
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@mikelove
Last seen 1 hour ago
United States

You won't be able to make a DESeqDataSet without the count data. If you just have FPKM/TPM this is going to be hard for you.

You can convert all to TPM and then consider other tools for batch correction and normalization.

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Michael Love - Can you please suggest some right tools to be used for the fpkm to tpm conversion..

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Multiplication. It's just making the FPKM for a sample sum to 1e6 over genes. But this is also not part of the scope of DESeq2. You can try biostars for general bioinformatics questions.

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Thank you!

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