[BioC] General normalization problem that's *similar* to microarrays.

Wolfgang Huber huber at ebi.ac.uk
Sat Dec 6 15:03:29 CET 2008

Alex Bokov ha scritto:
> Hello. I am examining data from a 2D gel experiment, but my question is 
> about a broader issue of normalization.
> Each gel has been stained with two different dyes, whose respective 
> intensities report two different protein features, let's call them A and 
> B. The quantity of interest is A/B. The data consists of two 
> protein-by-gel matrices of intensities, and I need to normalize them. 
> The questions is, which of the following would be the preferrable choice?
> 1) First do normalize.quantiles() on the A and B matrices individually 
> and then calculate A/B.
> 2) First calculate A/B and then do normalize.quantiles() on that.
> Thank you so much!

Dear Alex

have you checked whether it actually makes a difference - and if so, in 
what way?

Best wishes

Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

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