T-test analysis for gene expression comparison

Question

[Nithya]

Hi there, I would like to perform a t-test to evaluate the gene expression level between the mutation and normal groups. Can anyone prefer a suitable package and guidelines?

[rpolicastro]

What type of analysis is this?

[Nithya]

A statistical student's t-test to compare gene expression levels between normal and mutation tissue samples.

Answer 1

[swbarnes2]

You can't publish with a t-test result, it's just not a smart enough way to handle the math involved.

Do what everyone does. Run DESeq2 or EdgeR in R.

[bioinformatics2020]

THIS! You need to go back and learn about what type of distribution is used for a t-test. Then start understanding the distributions that gene expression data follows. This will give you a quick insight as to why you cannot use a t-test, and why the tools swbarnes2 posted about are needed.