raw count data- normalization

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6.5 years ago

ghmdsr ▴ 70

I got raw count data,which would consist of 32 samples and 20000 genes. With this data, I have to normalize this.

First step: normalized gene expression values per sample.

Second step: gene-wise normalization

Question 1: what is gene-wise normalization?

Question 2: how can I this two step?

I'm beginner, but no one can help me in my workplace. Please help me.

RNA-Seq gene • 2.4k views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 6.5 years ago by ghmdsr ▴ 70

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I recommend reading the documentation of DESeq2, a framework for differential RNA-seq analysis. It also includes a count normalization approach, using the estimateSizeFactors() function, which will give you a per-sample size factor that you can use to divide each sample by. There is a nice StatQuest video about this here. Other normalization approaches include TPM or FPKM normalization, depending on what you want to do with your data. Please give some details.

ADD REPLY • link 6.5 years ago by ATpoint 85k

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