Dear all, I am running RMA and MAS5 on some U133_Pluss_2 array and get this warning message : > x.rma <- as(rma(ab), "ExpressionSet") Warning messages: 1: missing or mis-shaped 'se.exprs' in original object; creating ExpressionSet without se.exprs in: asMethod(object) 2: contents of varLabels ignored > x.mas <- as(x.mas, "ExpressionSet") Warning messages: 1: missing or mis-shaped 'se.exprs' in original object; creating ExpressionSet without se.exprs in: asMethod(object) 2: contents of varLabels ignored I used these code lines: fnames <- paste(as.character(pData(pd)$ArrayName), "CEL", sep=".") ab <- read.affybatch(filenames=fnames, phenoData=pd, description=miame) x.mas <- as(x.mas, "ExpressionSet") x.rma <- as(rma(ab), "ExpressionSet") Background correcting Normalizing Calculating Expression R version 2.4.1 (2006-12-18) i686-pc-linux-gnu other attached packages: hgu133plus2cdf ClassDiscovery cluster ClassComparison PreProcess "1.14.0" "1.3" "1.11.4" "1.3" "1.3" oompaBase xtable colorspace geneplotter annotate "1.3" "1.4-3" "0.95" "1.12.0" "1.12.1" simpleaffy genefilter survival affy affyio "2.4.2" "1.12.0" "2.30" "1.12.2" "1.2.0" Biobase "1.12.2" Highly appreciate any comments! Caimiao Wei UT M.D.Anderson Cancer Center 1515 Holcombe Blvd, Unit 237 Houston, TX 77030-4009

Hi -- The version of affy you're using creates an 'se.exprs' slot with, I think, a zero-dimension matrix. Biobase ExpressionSet has become more picky about what se.exprs should look like, and in particular is should have the same number of features and samples as exprs. So the warning says that ExpressionSet took a particular action -- removed the 'empty' se.exprs -- rather than create an invalid instance. The warning about varLabels is similar, i.e., ExpressionSet doesn't know what to do with the information. The current version of Biobase and affy are back to thinking the same about their data representation, and in fact rma produces an ExpressionSet (despite what the documents say!): > library(affy) > example(rma) rma> data(affybatch.example) rma> eset <- rma(affybatch.example) Background correcting Normalizing Calculating Expression > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 150 features, 3 samples element names: exprs phenoData sampleNames: 20A, 20B, 10A varLabels and varMetadata: sample: arbitrary numbering featureData featureNames: A28102_at, AB000114_at, ..., HG2188-HT2258_at (150 total) varLabels and varMetadata: none experimentData: use 'experimentData(object)' Annotation [1] "" > sessionInfo() R version 2.5.0 Patched (2007-04-24 r41305) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: affy affyio Biobase "1.14.0" "1.4.0" "1.14.0" caiwei at mdanderson.org writes: > Dear all, > > I am running RMA and MAS5 on some U133_Pluss_2 array and get this warning > message : > >> x.rma <- as(rma(ab), "ExpressionSet") > Warning messages: > 1: missing or mis-shaped 'se.exprs' in original object; creating > ExpressionSet without se.exprs in: asMethod(object) > 2: contents of varLabels ignored > >> x.mas <- as(x.mas, "ExpressionSet") > Warning messages: > 1: missing or mis-shaped 'se.exprs' in original object; creating > ExpressionSet without se.exprs in: asMethod(object) > 2: contents of varLabels ignored > > I used these code lines: > > fnames <- paste(as.character(pData(pd)$ArrayName), "CEL", sep=".") > ab <- read.affybatch(filenames=fnames, phenoData=pd, description=miame) > > x.mas <- as(x.mas, "ExpressionSet") > x.rma <- as(rma(ab), "ExpressionSet") > Background correcting > Normalizing > Calculating Expression > > > R version 2.4.1 (2006-12-18) > i686-pc-linux-gnu > > other attached packages: > hgu133plus2cdf ClassDiscovery cluster ClassComparison > PreProcess > "1.14.0" "1.3" "1.11.4" "1.3" > "1.3" > oompaBase xtable colorspace geneplotter > annotate > "1.3" "1.4-3" "0.95" "1.12.0" > "1.12.1" > simpleaffy genefilter survival affy > affyio > "2.4.2" "1.12.0" "2.30" "1.12.2" > "1.2.0" > Biobase > "1.12.2" > > > Highly appreciate any comments! > > Caimiao Wei > > UT M.D.Anderson Cancer Center > 1515 Holcombe Blvd, Unit 237 > Houston, TX 77030-4009 > > _______________________________________________ > 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