Conversion from FPKM,RPKM to tpm
1
0
Entering edit mode
Sandhiya • 0
@8bdd529f
Last seen 25 days 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 • 293 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 22 hours 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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you!

ADD REPLY

Login before adding your answer.

Traffic: 267 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6