This will be the most unintelligent question asked here but since I am new to microarray analysis I have mandatory authorization to ask this kind of question :D
I could not find any informations about it so far maybe I asked wrong, but what is the difference between AgilentG4502A_07_2 and AgilentG4502A_07_1? I just found out that they have different features and I can't preprocess both of them together with read.maimages().
It would be really nice to find out the difference and how can I process them both together.
It's not an unintelligent question per se, but it's not asked in the right place. This isn't an Agilent support site, so there is no reason to suspect that anybody here has an answer for you. In addition you have already found that they have different features, so haven't you already answered your own question?
If they have different features, why would you want to process them together? The rationale behind processing a set of arrays together is that they are identical except for different samples, and possibly small technical differences. You don't have that, so why force the issue?
AgilentG4502A_07_2 and AgilentG4502A_07_1 seem to be custom arrays mentioned on the National Cancer Institute website. Custom arrays are made to order by Agilent, according to a requested set of probes. So the only people who will know what they are are Agilent and whoever ordered them. Details are presumably on the NCI website.
Usually one cannot combine data from different microarray platforms. Occasionally one can do an ad hoc consolidation of arrays that differ only in a small number of probes. However, if you are new to microarray analysis, you shouldn't be attempting that.
