Question: Which normalization is good for gene expression classification and clustering
2
gravatar for Maryam
3 months ago by
Maryam40
Maryam40 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 3 months ago • written 3 months ago by Maryam40
1
gravatar for ATpoint
3 months ago by
ATpoint12k
Germany
ATpoint12k wrote:

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

ADD COMMENTlink written 3 months ago by ATpoint12k

so many thanks for your reply

ADD REPLYlink written 3 months ago by Maryam40
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