I will work on comparison of expression profiles from two different lymphoblastoid cell lines with particular disrupted genes in order to explore affected pathways. The array is Human GE 4x44K v2 Microarray. Additionally, I will use RNA from peripheral blood as control. Thanks in advance.
For the 4x44k arrays it doesn't matter much. If you want a higher dynamic range, go for one-color. If identifying regulted genes is sufficient, you may save some money with the two-color hybridizations in a balanced dye-swap design (i.e. the same number of samples from each groups is labelled in either color to avoid dye-bias).
The 8x60k arrays donn't work well for two-color hybs (at least in our hands). I suppose the spots are so small that competition effects in target binding becomes relevant, further squeezing and distroting the measured differential profiles.
It seems that the two-color hybs issue happens in other places too, because you are the second person telling me the same thing in these days. I think I will use the one-color protocol. Thank you very much for your answer. =)
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