Question

Quantile normalization and Deseq2

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lirongrossmann ▴ 80

@lirongrossmann-13938

Last seen 4.2 years 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 • 2.7k views

ADD COMMENT • link updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by lirongrossmann ▴ 80

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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).

ADD REPLY • link 7.2 years ago lirongrossmann ▴ 80

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Yes, the counts are comparable after normalization and transformation.

ADD REPLY • link 7.2 years ago Michael Love 43k

score 0 · Answer 1 · 2017-10-27

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Michael Love 43k

@mikelove

Last seen 4 days ago

United States

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

ADD COMMENT • link 7.2 years ago Michael Love 43k