RNA Seq FAQ: What if the gene was never present/expressed in control sample?

Question

[Dr SKY]

This is a very simple question and forgive me for sounding dumb in this case What if a gene was never expressed in the control sample? How do you determine the expression value change in treated condition using RNA Seq (if the gene expressed only under treated condition)? Will the gene be considered as novel?

Answer 1

[ATpoint]

Most tools use prior counts to avoid computing infinite fold changes.

You can get more information by starting with these answers from the developers of DESeq2 and edgeR:

For DESeq2: https://support.bioconductor.org/p/64014/

For edgeR: https://support.bioconductor.org/p/57440/

[Dr SKY]

Thank you for your response.