[BioC] marray intensity normalization?

Jake Michaelson jjmichael at comcast.net
Thu Jun 16 22:29:59 CEST 2005

Hi all,

I'm a little more familiar with single-channel chips (Affy) than I am 
with spotted two-color arrays, and I'm now starting to get involved 
with the analysis of some two-color arrays.

I was wondering (thinking of this from the single-channel mentality) if 
there's a way to use marray (or another package) to get normalized 
intensities of each channel, rather than log-ratios; this would 
essentially treat each channel like an individual single-channel chip.

I'd like to then convert these normalized intensities into an exprSet, 
with two intensities per chip.  In other words, if I had 12 two-color 
chips, I'd like to end up with a 24-column exprSet.

Somebody please stop me in my tracks if I'm heading into dangerous 
waters by using a single-channel mentality with two-color chips!



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