hi, i am doing one color agilent arrays..i have three groups,GROUP1,GROUP2,GROUP3 and each group has 4 replicates.i made contrast matrix using limma.Is this possible to analyse data by RankProd using same contrast matrix. i want to make comparison by RankProd as GROUP1 vs GROUP2 GROUP1 vs GROUP3 GROUP3 vs GROUP2 plz let me know if there is any way to do it in single command using RankProd as we can do it in limma. this is the R-script i used. targets SampleNumber FileName Condition 1 1 K_BNG202_251485068094_1.txt GROUP1 2 2 K_BNG211_251485067236_1.txt GROUP1 3 3 K_BNG252_251485068096_1.txt GROUP1 4 4 K_BNG263_251485068028_1.txt GROUP1 5 5 P_BNG019_251485068025_3.txt GROUP2 6 6 P_BNG039_251485066211_1.txt GROUP2 7 7 P_BNG065_251485068023_4.txt GROUP2 8 8 P_BNG076_251485068021_4.txt GROUP2 9 9 V_BNG264_251485068028_2.txt GROUP3 10 10 V_BNG271_251485068092_1.txt GROUP3 11 11 V_BNG_043_251485037342_2.txt GROUP3 12 12 V_BNG_089_251485037359_3.txt GROUP3 > colnames(y.q[j,]) [1] "K_BNG202_251485068094_1" "K_BNG211_251485067236_1" "K_BNG252_251485068096_1" [4] "K_BNG263_251485068028_1" "P_BNG019_251485068025_3" "P_BNG039_251485066211_1" [7] "P_BNG065_251485068023_4" "P_BNG076_251485068021_4" "V_BNG264_251485068028_2" [10] "V_BNG271_251485068092_1" "V_BNG_043_251485037342_2" "V_BNG_089_251485037359_3" > design <- model.matrix(~0 + f) Error in eval(expr, envir, enclos) : object 'f' not found > f <- factor(targets$Condition, levels = unique(targets$Condition)) > design <- model.matrix(~0 + f) > colnames(design) <- levels(f) > contrast.matrix <- makeContrasts("GROUP1-GROUP2", "GROUP2-GROUP3", "GROUP3-GROUP1", levels=design) -- output of sessionInfo(): R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RankProd_2.30.0 limma_3.4.3 -- Sent via the guest posting facility at bioconductor.org.