Question: Using a chi-squared test for independence for DEG analysis
gravatar for SylviaR
10 days ago by
SylviaR0 wrote:


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!

ADD COMMENTlink modified 5 days ago • written 10 days ago by SylviaR0

Thank you so much! :):)

ADD REPLYlink written 5 days ago by SylviaR0
gravatar for ATpoint
10 days ago by
ATpoint19k wrote:

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.

ADD COMMENTlink written 10 days ago by ATpoint19k
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