Hi, I am having some problems reading quantarray files in Limma. I can read the files and perform the analysis but after I finish the analysis and try to visualize the results using the function topTable I don't see the IDs of my genes. Any help is appreciated. The code I am using is: library(marray) library(limma) library(convert) #read target info again (in a format that limma will understand) targets <- readTargets("target.txt") #read data data2 <- read.maimages(targets$FileName, source="quantarray") #normalize data within arrays MA <- normalizeWithinArrays(data2, method = "median") #normalize between arrays MA.loess <- normalizeWithinArrays(data2, method="loess") #statistical analysis design <- modelMatrix(targets, ref="FSEM") fit <- lmFit(MA.loess, design) fit2 <- eBayes(fit) topTable(fit2, n=24) The results I get are something like this: Array.Row Array.Column Row Column Name logFC AveExpr t P.Value adj.P.Val B 2979 1 4 4 3 NA 0.7650399 11.317572 10.440014 5.369919e-07 0.02477036 5.720621 10025 3 3 14 12 NA 1.1112795 11.607394 9.107978 2.053595e-06 0.04430252 4.764422 6803 2 4 3 14 NA 1.4909917 10.853941 8.794212 2.881277e-06 0.04430252 4.511043 6701 2 3 31 5 NA 0.8038261 10.822350 8.447169 4.237030e-06 0.04447141 4.216955 1848 1 2 29 19 NA 0.6509226 10.366205 8.333438 4.820435e-06 0.04447141 4.117292 40791 11 3 14 26 NA -0.4895443 10.247273 -7.356528 1.545782e-05 0.07290949 3.189524 6143 2 3 13 5 NA 0.6494603 10.863728 7.295153 1.669200e-05 0.07290949 3.126713 13769 4 3 11 5 NA 0.9898807 13.038236 7.178328 1.934401e-05 0.07290949 3.005600 3544 1 4 22 10 NA 0.5205167 10.318964 6.871036 2.873648e-05 0.07290949 2.677103 Best regards, -- Michael Waisberg, MD, PhD Visiting research fellow Laboratory of Immunogenetics Twinbrook II, National Institute of Allergy and Infectious Diseases Rockville, MD 20852 _________________________________________ "I do not fear computers. I fear the lack of them." Isaac Asimov [[alternative HTML version deleted]]