Hello, I'm learning (slowly) the way eSet and ExpressionSet classes work. What I want to do is probably quite simple, but I can't figure out the following: how do I either display (onscreen) or write into a file the expression levels of an ExpressionSet object AND include some or all featureData? For example, in the ExpressionSet generated below I have g1-g5 replicated 4 times, and pos1-pos2 is replicated 10 times: set.seed(31415) exprs=data.frame(matrix(rnorm(100),nrow=20, ncol=5)) colnames(exprs)=letters[1:5] pData=data.frame(matrix(rbinom(15,1,.5), nrow=5, byrow=T)) rownames(pData)=letters[1:5] colnames(pData)=c("sex","agegrp","location") phenoData=new("AnnotatedDataFrame", data=pData, varMetadata=c("Gender","Age Group", "Location")) fNames=rep(c("g1","g2","g3","g4","g5"),4) fLoc=sort(rep(c("pos1","pos2"),10)) fData=data.frame(name=fNames, location=fLoc) fDatalbl=data.frame(labelDescription=c("Name of Gene", "Location of Gene"), row.names=colnames(fData)) featureData=new("AnnotatedDataFrame", data=fData, varMetadata=fDatalbl) data=new("ExpressionSet", exprs=exprs, phenoData=phenoData, featureData=featureData) > data ExpressionSet (storageMode: lockedEnvironment) assayData: 20 features, 5 samples element names: exprs phenoData rowNames: a, b, ..., e (5 total) varLabels and varMetadata: sex: NA agegrp: NA location: NA featureData rowNames: 1, 2, ..., 20 (20 total) varLabels and varMetadata: name: Name of Gene location: Location of Gene experimentData: use 'experimentData(object)' Annotation character(0) I'd like to get something like this using some accessor function (is there one?): fNames fLoc a b c d e 1 g1 pos1 1.64701 0.87221 -2.19476 -0.46615 1.01645 2 g2 pos1 -1.11199 1.05936 1.28965 -0.61097 -0.41773 3 g3 pos1 -1.54855 0.48339 -0.46200 1.17314 -0.09009 4 g4 pos1 -0.74838 -1.46186 0.35942 -0.87757 -1.33541 5 g5 pos1 1.52641 -0.39533 0.07781 1.26703 0.71262 6 g1 pos1 -1.13793 0.36251 0.45685 0.19561 1.16690 The data set I'm working with comes from a custom array with 3 replicates for each gene, and thus the "feature" names are not unique. Am I setting up the ExpressionData object correctly? Is there a better way than to incorporate non-unique gene names in exprs than to use gene names via featureData? Thanks for any advice! Masha ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Masha Kocherginsky, Ph.D. Research Associate (Assistant Professor) Department of Health Studies University of Chicago 5841 S. Maryland Ave. Chicago, IL 60637 This email is intended only for the use of the individual or...{{dropped}}