Currently I'm trying to analyze a three-color experiment from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38522
I have no problem to read such file, but I don't know how to analyze this kind of chip. After checking their chip design, ctrl is not always on each chip, which suggest that probably differential expression require comparison between different channel from different chips. I think after they have done normexp background corrected and quantile normalized using limma, ComBat function was used for removing batch effect.(http://onlinelibrary.wiley.com/doi/10.1111/nph.12378/full)
So my question is,
if I treat the different channel from each chip as separated-single-channel, how to proceed normalization, with which package.
If not, how to normalize three-color-chip, but I think currently there is no suitable package can directly do that.
And I will be very grateful for all your answers and help.