What can I do with pan-cancer RNA-seq data that only has FPKM value?

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23 months ago

Brisket ▴ 10

I'm using the NCI-60 RNA-seq data to do my analysis, but fount that there is only an excel sheet with FPKM value in the database. Since most of the packages require raw count for normalization, is there a methods that can normalize the FPKM data for pan-cancer research?

normalization RNA-seq • 873 views

ADD COMMENT • link updated 23 months ago by ATpoint 85k • written 23 months ago by Brisket ▴ 10

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What is your analysis goal?

ADD REPLY • link 23 months ago by ATpoint 85k

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Just saw that previous post. I am windering what one could meaningfully do with 60 celllines. CLs are tools, their transcriptomes have adapted to existing outside of stromal context and in a dish. They will be very different from each other even if they’re from the same cancer entity. Wonder what you want to do with it. Probably not much to really get from such artificial data. FPKM is not a good measure as it fails to correct for composition differences that you certainly have here.

ADD REPLY • link 23 months ago by ATpoint 85k

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See my comment from today on your last post about this same topic: Pan-cancer RNA-seq data normalization

ADD REPLY • link 23 months ago by bkleiboeker ▴ 370

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