Hello, I have two questions and I hope you can help me. I want to compare several studies with similar design but different arrays. The first step was to quantile normalize all data which works well beside the two color experiment with an Agilent chip. I read the limma User Guide and find out that I must preprocess with the function normalizeBetweenArrays. So I get M- and A-values and my question is which one shows the expression values for this experiment? For comparing the results of the different studies I want to use the package: RankProd. For a better comparision between the studies I used the Entrez IDs and I download the last chip information directly from affymerix and illumina. So this reveal a new problem. For example on the chip Affymetrix Mouse Genome 430 2.0 Array the ID 1449880_s_at stands for three gene names and entrez ids:Bglap /// Bglap2 /// Bglap3 - 12095 /// 12096 /// 12097. On the Illumina Chip each gene has a single Array ID: Bglap-rs1 - ILMN_1233122 - 12095 Bglap1 - ILMN_2610166 - 12096 Bglap2 - ILMN_2944508 - 12097 So I don't no what I should do to compare the results of this two experiments. When I paste the expression values of 1449880_s_at three times with the three different entrez-IDs the ranking which was calculating with the RankProd-Package was changed. Example: Chip ID Entrez-Id Control1 control 2 etc. 1449880_s_at - 12095 - 3,855 - 4,211 ... 1449880_s_at - 12096 - 3,855 - 4,211 ... 1449880_s_at - 12097 - 3,855 - 4,211 ... The other possibility is to take the three expression Values of the illumina chip to one value. But I don't know if the is the right way. What is the better way? Kind regards Stefanie Busch