Quantile normalization + sva for microarray experiment
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Entering edit mode
@dimitrileonidlindenwald-7183
Last seen 5.7 years ago
Germany

Dear All,

I have a question regarding my analysis routine.

My dataset, a microarray experiment,was first normalized using quantile normalization, 
and then a supervized sva with microarray chip controls was performed to remove the unwanted variation.
As far as i understood, sva requires a normalized dataset.

My question: is it correct this way? Can sva be applied after quantile normalization, or is it somehow wrong?

Thank you in advance.

Best regards,

Dimitri 

 

sva quantile normalization microarray • 1.2k views
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3
Entering edit mode
Jeff Leek ▴ 610
@jeff-leek-5015
Last seen 4 months ago
United States

Hi Dimitri

Yes sva can be applied after quantile normalization and in fact is usually used after other pre-processing techniques have been applied. 

 

Best

 

Jeff

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