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Question: Quantile normalization and Deseq2
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gravatar for lirongrossmann
26 days ago by
lirongrossmann0 wrote:

 Hi all,

I am using variance stabilizing transformation on my rna seq count data with Deseq2.

Do I need to use quantile normalize the samples or does variance stabilizing transformation function take care of it?

 

ADD COMMENTlink modified 26 days ago by Michael Love15k • written 26 days ago by lirongrossmann0

Thanks, I just wanted to make sure that genes that have "low" counts in two samples are comparable (i.e. have similar rank for example).

ADD REPLYlink written 26 days ago by lirongrossmann0

Yes, the counts are comparable after normalization and transformation.

ADD REPLYlink written 26 days ago by Michael Love15k
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gravatar for Michael Love
26 days ago by
Michael Love15k
United States
Michael Love15k wrote:

What would be the reason for quantile normalization, beyond the sequencing depth normalization we already implement?

ADD COMMENTlink written 26 days ago by Michael Love15k
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