Search
Question: Quantile normalization and Deseq2
0
gravatar for lirongrossmann
7 months ago by
lirongrossmann10 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 7 months ago by Michael Love18k • written 7 months ago by lirongrossmann10

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 7 months ago by lirongrossmann10

Yes, the counts are comparable after normalization and transformation.

ADD REPLYlink written 7 months ago by Michael Love18k
0
gravatar for Michael Love
7 months ago by
Michael Love18k
United States
Michael Love18k wrote:

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

ADD COMMENTlink written 7 months ago by Michael Love18k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 231 users visited in the last hour