Question: Which normalization is good for gene expression classification and clustering
gravatar for Maryam
4 weeks ago by
Maryam20 wrote:

Hi All, I have gene expression (raw count and FPKM) from healthy and disease states. I'm going to do supervised and unsupervised classification on gene expression. As dimension reduction I'm going to get differential expression genes from DESeq2 and use these genes as features in my classification.
The problem is that I don't know which normalization is good in the classification study? Is it good to use FPKM? What about using DESeq2 normalization?

I would appreciate if someone could advise me, Many thanks

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Maryam20
gravatar for ATpoint
4 weeks ago by
ATpoint9.3k wrote:

rlog and vst are recommended options. Check the DESeq2 manual for details.

ADD COMMENTlink written 4 weeks ago by ATpoint9.3k

so many thanks for your reply

ADD REPLYlink written 4 weeks ago by Maryam20
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