Hi all, I am extremely new at R and microarray analysis and so some of my questions may sound silly but I do hope someone will be able to help. I am analyzing Agilent one colour custom 4x44k array data. My targets file is labelled as: FileName Cy3 1 control1 2 control1 3 mutant1 4 mutant2 5 control1 6 control2 7 mutant1 8 mutant2 where I have 3 technical replicates and 2 biological replicates of my control, 2 biolrep of mutant 1 and 2 biolrep of mutant 2. i.e. As such how do I define my design matrix? Secondly how do I convert my data to an exprSet object so that I can analyse it like a Affymetrix array? As a sidenote, I have already created my MA object and tried to fit it as: > fit<-lmFit(MA) > fit<-eBayes(fit) But I get an error: Error in if (evar > 0) { : missing value where TRUE/FALSE needed In addition: Warning message: In fitFDist(var, df1 = df) : More than half of residual variances are exactly zero: eBayes unreliable Any idea what was wrong with my data? I am sure this is some silly formatting error that i must have missed out. Thank you in advance. Cheers Wendy [[alternative HTML version deleted]]