Hi Masha -- What you'd like to do is bind the columns of the pData of featureData to the expression data (and just show the first few lines): > head(cbind(pData(featureData(data)), exprs(data))) name location a b c d e 1 g1 pos1 1.6470129 0.8722101 -2.19475753 -0.4661532 1.01644889 2 g2 pos1 -1.1119872 1.0593626 1.28964663 -0.6109748 -0.41772721 3 g3 pos1 -1.5485456 0.4833932 -0.46199812 1.1731445 -0.09008735 4 g4 pos1 -0.7483785 -1.4618555 0.35941850 -0.8775726 -1.33541208 5 g5 pos1 1.5264111 -0.3953324 0.07780542 1.2670281 0.71261880 6 g1 pos1 -1.1379254 0.3625114 0.45684852 0.1956062 1.16690297 If you'd wanted to create the equivalent structure but with phenoData, then as.data.frame(data) would have done this for you. A couple of other comments... > phenoData=new("AnnotatedDataFrame", data=pData, > varMetadata=c("Gender","Age Group", "Location")) I think varMetadata should be a data frame with a (required) column called 'labelDescription', e.g, > varMetadata=data.frame(labelDescription= + c("Gender","Age Group", "Location")) > phenoData=new("AnnotatedDataFrame", + data=pData, varMetadata=varMetadata) Depending of course on how involved you want to get, the 'annotation' slot of ExpressionSet is meant to reference an annotation package that contains information about features, e.g., maps between (unique) probe names and (possibly repeating) gene names. This is easy for standard chips, since the annotation packages already exist. More challenging for custom chips, where you have to create the annotation package yourself. Worth figuring out if you'll use the same chip design many times -- the mapping just has to be done once, in creating the annotation package. Hope that helps, Martin "Kocherginsky, Masha [BSD] - HSD" <mkocherg at="" health.bsd.uchicago.edu=""> writes: > 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}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org