[BioC] limma question

[leon ding]

 Hello everyone.
=20
I am currently evaluating difference between one-color and  two-color hybri=
dization to decide which one should be used for upcoming project. For 2-col=
or, I found in my self vs self hybs, the gene-specific cy5/cy3 bias (i.e., =
reproducible red or green spots on self-self slides) is quite significant. =
This will affect the real sample-control experiments especially if the fold=
 changes of differential _expression is small. A compensate solution is to =
divide the ratio of sample-control slides to control-control slides. Althou=
gh there is no reference RNA samples, the "Two-Sample Experiments" medel in=
 limma may fit very well for this purpose. ( I appreciate to hear your opin=
iones on this).An alternative is to use single color hyb, one is control an=
d another is sample, and this will cut half of the labor and cost. But can =
limma handle one-color experiments? If not, is there any good packages for =
single color normalization and significance analysis? My guess is that it w=
ill have to involve scaling and wonder if it can generate similar results a=
s 2-color experiment.
=20
Leon




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