Question: Which normalization is good for gene expression classification and clustering
3
gravatar for Sara
22 months ago by
Sara60
Sara60 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 22 months ago • written 22 months ago by Sara60
1
gravatar for ATpoint
22 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

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

ADD COMMENTlink written 22 months ago by ATpoint36k

so many thanks for your reply

ADD REPLYlink written 21 months ago by Sara60
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