Quantile normalization and Deseq2
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@lirongrossmann-13938
Last seen 9 months ago

 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?

 

quantile normalization deseq2 • 1.2k views
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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).

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Yes, the counts are comparable after normalization and transformation.

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@mikelove
Last seen 4 days ago
United States

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

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