[BioC] two-color single channel preprocessing problems

[Giulio Di Giovanni]

Hi group,

I'm trying to preprocess some two-colours single-channel slides. Looking 
through the mailing list archives I found some suggestions. But I still have 
some doubts...

1) first of all, a very basic question. In our group we came to the decision 
to simply don't consider the second channel (green) and to make all the work 
(BGcorrect, norm, etc) on the only one used (red). Is it right ?

2) Looking at the background images we found a clear block effect, and also 
a kind of gradient through the three subarrays we have for each slide. Do 
you is possible/useful try to remove this effect with a linear model (I mean 
a simple  lm(signal~block) or lm(signal~block+ row + col...) , or there are 
already correction methods in BioC that can be efficiently applied for these 
purposes (both, the block effect mainly but the gradient to) ? Which ones ?

Thanks a lot in advance,

Regards

Giulio

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