1 ve 2 dye arrays - (Aug/15/2008 )

I have purchased a set of custom oligo arrays that I plan on using in the next few months. I have the option of performing either 1 dye or 2 dye hyb with these arrays. I am considering going with the 1 dye system (using Cy-3) as it will allow me to generate ratios for samples from any 2 slides. However, I am wondering, is it acceptable to generate ratio data with samples hyb'd to different slides using the 2 dye system. I am assuming not as "competition" for the oligo will vary from slide to slide depending on samples? If I were to use a common reference sample on all slides would I then be able to generate ratios for samples on different slides.

Cost is not really an issue for me, just want to find the "best" way of doing this.

Thanks!

I am using 1 dye microarray platform and i have no problem at all to get data.
I believe that 1 dye is better coz it eliminates dye bias and you do not need to extract too much of your control sample to hyb every chip.
I used a commercial software available in my institute to analyze my data. The software was purchase long before we started 1 dye microarray (we use 2 dyes previously). The analysis was good. If you have a software like that, maybe you can consult the software developer to check if the software suitable for your experiment.

Hi,

I am not sure whether you have known about MAQC project (Microarray Quality Control). One-color and Two-color platforms efficiency have been validated here. Find the article given below:

Nature Biotechnology: 2006 Sep;24(9):1140-50
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.

Hope this would help you choose.