Using a chi-squared test for independence for DEG analysis

Question

[SylviaR]

Hi,

I have an expression matrix of data from three different conditions (about 75 samples in total, 25 for each condition). To identify differentially expressed genes, is it possible to do a chi-squared test for independence, comparing the groups? So I compare group A to B, B to C and C to A.

Is this advisable, if so, why not and what should I do in stead?

Thank you so much!

[SylviaR]

Thank you so much! :):)

Answer 1

[ATpoint]

Use any of the established tools such as DESeq2, edgeRor limma. Please read the respective papers to see why these specialized methods exist and how they compare to naive approaches.