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Using a chi-squared test for independence for DEG analysis

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!

rna-seq rna-seq sequence next-gen sequencing
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written by SylviaR • SylviaR

Thank you so much! :):)

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written by SylviaR • SylviaR

1 answer

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.

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written by ATpoint ATpoint

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