[BioC] Design/Contrast for Two-Channel Experimental Setup

Joseph Shaw josph.sh at gmail.com
Wed Jan 8 00:51:34 CET 2014

Dear Gordon,

> It is probe-specific, as I said before.  No one claimed it was "observation
> specific".

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.

Kind regards,


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