Hello, I am analyzing microarray data and i am little bit new to R programming. it has 4 different sample with 3 replicate each. I went upto background correction but i found difficult in normalization and getting duplicate correlation. can you help me in further process Thank you in advance. library(limma) > getwd() [1] "/Users/nirajnepal/Documents/codata" > datadir <- system.file("codata") > library(RColorBrewer) > targets <- readTargets("targets.txt") > cols <- brewer.pal(12, "Set3") > RG <- read.maimages(targets$FileName, source="genepix", columns=list(Rf="F635 Mean",Gf="F635 Mean",Rb="B635 Median",Gb="B635 Median")) Read Cnt.1.gpr Read Cnt.2.gpr Read Cnt.3.gpr Read Day1.1.gpr Read Day1.2.gpr Read Day1.5.gpr Read Day3.1.gpr Read Day3.2.gpr Read Day3.3.gpr Read Day90.2.gpr Read Day90.3.gpr Read Day90.4.gpr > pData <- data.frame(population = c('a', 'a', 'a','b', 'b', 'b','c','c','c','d','d','d')) > rownames(pData) <- RG$targets$FileName > design <- model.matrix(~factor(pData$population)) > gene <- grep("GE", RG$genes$ID) > RG.final <- RG[gene, ] > boxplot(data.frame(log2(RG.final$Rb)),main="Background", col=cols) > boxplot(data.frame(log2(RG.final$R)),main="Foreground", col=cols) > RGb <- backgroundCorrect(RG.final, method="subtract") > boxplot(data.frame(log2(RGb$R)),main="Backgroud Correction", col=cols) There were 13 warnings (use warnings() to see them) > library(Biobase) > library('vsn') > y2 <- normalizeVSN(RGb$R) vsn2: 35891 x 12 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > boxplot(as.data.frame(log2(y2)), main="Normalized intensities", col=cols) > corfit <- duplicateCorrelation(y2, design, ndups=3) Loading required package: statmod Error in dim(M) <- c(spacing, ndups, ngroups, nslides) : dims [product 430668] do not match the length of object [430692] -- *Niraj Nepal* * Research Assistant * *Cell and Molecular Physiology Lab* *West Virginia Sta**te University* *Institute, WV* [[alternative HTML version deleted]]