Hi Paul, I am trying to follow the your "Read single channel GenePix in limma " version of code for my data. I could able to run properly till "VSN normalization" but after that when I am running the duplicateCorrelation I am getting warnings. These are the sequences of steps that I did starting normalization. mat <- vsnMatrix(RG.final$G) bb <- as.matrix(mat) rownames(bb) <- RG.final$genes$Name bb <- bb[order(rownames(bb)), ] corfit <- duplicateCorrelation(bb, design, ndups=4) There were 50 or more warnings (use warnings() to see the first 50) Warnings are : 50: In sqrt(dfitted.values) : NaNs produced So can you please help me out in this regard. Thanks Ashwin This email is intended only for the use of the individua...{{dropped:12}}

Is it possible to compare just two arrays, I mean what if we have arrays A1, A2 and compare A1 vs A2. Thanks Ashwin This email is intended only for the use of the individua...{{dropped:12}}