What are Differentially Expressed Genes ?!!

What are Differentially Expressed Genes ?!!

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Hi,

Believe me, I know what I am going to ask would sound stupid and repetitive. I did read through many of the articles available but still is confused.

So, let’s say I am doing an RNA-seq DEG analysis with a dataset of 4 samples, each two of them belong to the group of Control and Treated. I have the quantification results and would like to perform DEG analysis. I have a couple of doubts:

  1. Which data would be called as expressed genes ?
  2. Which set of genes would be called as Differentially Expressed Genes ? From what I understood the genes in the count file would undergo normalisation and the resulting genes screened with the FDR<0.05 and logFC threshold are called Differentially expressed. Please correct me if I am wrong.
  3. Which parameter should I consider to select the DEGs? I read that most commonly used is FDR<0.05 and logFC, but somewhere else Pvalue<0.05 is also mentioned.
  4. Somewhere I found that all the genes expressed are Differentially expressed and the PValue and logFC cutoff is done to select the significant DEGs. Is that the concept ?

I hope someone would help me to solve my confusions.

Thank you.


FDR


pvalue


logFC


expressioncounts


DEG

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