Question: raw count data- normalization
gravatar for ghmdsr
20 months ago by
ghmdsr30 wrote:

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

Question1 : what is gene-wise normalization? Question2 : how can i this two step?

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

rna-seq tutorial gene • 1.0k views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 20 months ago by ghmdsr30

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 REPLYlink written 19 months ago by ATpoint28k
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