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5.0 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.
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.