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 

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