Question: Which normalization is good for gene expression classification and clustering
2
gravatar for Maryam
16 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 16 months ago • written 16 months ago by Maryam40
1
gravatar for ATpoint
16 months ago by
ATpoint29k
Germany
ATpoint29k wrote:

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

ADD COMMENTlink written 16 months ago by ATpoint29k

so many thanks for your reply

ADD REPLYlink written 16 months ago by Maryam40
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