What is the basis of differential expression in RNA-seq?

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5.5 years ago

masicioglu ▴ 10

Hi All,

I want to ask about RNA-seq normalisation. I read about TMM- normalisation (EdgeR) or Median of ratios (DeSeq2) much correct rather than TPM, RPKM to compare expression levels between two group. Simply, I wonder what is the basis of TMM-normalisation or median of ratios?

Thanks,

Meltem

RNA-Seq • 838 views

ADD COMMENT • link updated 5.5 years ago by ATpoint 82k • written 5.5 years ago by masicioglu ▴ 10

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Hi masicioglu,

welcome to Biostars. This question is far more extensive than you may think and has been addressed both here on Biostars as well as in multiple blogs and publications. I would start with this video on DESeq2 normalization and these two publications A and B. Once you have an overview about the general concepts, feel free to come back with a more specific question.

ADD REPLY • link 5.5 years ago by ATpoint 82k

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These advices were very helpful. Thanks a lot!

ADD REPLY • link 5.5 years ago by masicioglu ▴ 10

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