[BioC] Separating channels of a two-color microarray

[January Weiner]

Dear all,

first, I would like to thank all who answered my questions in the past.

I am attempting a meta-analysis of several microarray studies, with
limma as my working horse. I plan to throw all the microarrays
together, creating one large data set with one of the factors in the
analysis being the data set. Preliminary analyses with a limited
number of studies are encouraging; on one hand, I am able to reproduce
the results of the single studies, while at the same time finding
robust differences between the studies (and their respective cohorts).

However, I hit a wall with one of these studies, which involved
two-color Agilent chips, not with a common reference, but each chip
corresponding to two different individuals from two experimental
groups. For some of the analyses that I plan I need separate
intensities for each experimental group -- fold changes won't cut it
(for example, in case of machine learning in which I use the
intensities to construct a model for predicting the group
assignments).

I  tried to directly use the R and G channels, and the results are
actually quite good. Of course, this is not an optimal approach.
Normally, when faced with two-color arrays and a complex experimental
design I use intraspotCorrelation and lmscFit.

Question: is there a way to use the results of intraspotCorrelation to
correct the R and G channels?

Kind regards,
j.

-- 
-------- Dr. January Weiner 3 --------------------------------------