[BioC] Design/Contrast for Two-Channel Experimental Setup
josph.sh at gmail.com
Wed Jan 8 00:51:34 CET 2014
> It is probe-specific, as I said before. No one claimed it was "observation
My apologies - I didn't mean to imply that anybody had claimed the
above. I was just hoping to eliminate some ambiguities that I had
> Well, first off, your code never did between-array normalization, because
> the between-array command produced a data object that was not used in the
> subsequent analysis.
Oh, I see. That was actually a typo - it was my intention to use the
resulting data object.
> Your understanding about between array normalization might be from
> experience with single channel arrays. For two colour arrays, the loess
> normalization step already puts the M-values for different arrays on a
> common scale so there is (usually) nothing more to do. Loess normalization
> is superior to quantile normalization because it uses the pairing of channel
> values from the same spot. A subsequent quantile normalization step is not
> needed and would mess up the job done by loess normalization.
That makes a lot of sense. Thanks for clearing that up.
> Also, I would not describe quantile normalization as a "scaling" procedure.
I agree. It was definitely a clumsy phrasing; I meant it in terms of
inducing a degree of uniformity.
Thank you once again for all your assistance - it's greatly appreciated.
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