Does anyone explain step by step how obtain Fc from Tmm normalizatio count???

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4.1 years ago

g.persic1991 ▴ 10

Hi guys, I'm very confused about edgeR. I have read the paper and i understand how TMM normalization were done....but from here to logFC calculation of DE, is very hard for me... Please...Could you help me, explaining edgeR with a simple example. I'm interesting in particular to glm-edgeR.

Thanks in advance Giuseppe

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ADD COMMENT • link 4.1 years ago by g.persic1991 ▴ 10

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Why don’t you let edgeR do the calculations by simply running the standard code from the manual?

ADD REPLY • link 4.1 years ago by ATpoint 85k

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because, I'd like to know which steps are behind edgeR-glm. Analysis was already done, results seems good but i think is crucial to know what you are doing to be sure of them.

Giuseppe

ADD REPLY • link 4.1 years ago by g.persic1991 ▴ 10

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If you want to be sure about what is being done, I think you will need to read the relevant papers and the edgeR source code.

ADD REPLY • link 4.1 years ago by h.mon 35k

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