[BioC] marray intensity normalization? dangerous waters

Simon Lin simon.lin at duke.edu
Thu Jun 23 00:01:05 CEST 2005


Sport fans might like dangerous waters. 8-)

To the topic, I have anecdotal evidence that glass-slide array can actually 
be one-color, if your printing quality is very good.

With such a high quality array, I did not see any difference by sticking to 
R/G ratios, or treat them the single-channel way.


>>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.

>>Somebody please stop me in my tracks if I'm heading into dangerous
>>waters by using a single-channel mentality with two-color chips!
> You are heading in very dangerous waters indeed and, almost certainly, you
> don't really want to do it. If you change your technology, you need to
> change you thinking as well. The red-green pairing is the whole point of
> the two-colour technology and you cannot ignore it without drastic loss of
> accuracy.

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