Hello All, I wrote a script to analyse affymetrix data but its giving an error while using the topTable from limma: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type I checked all the steps that might be causing the error but couldn't find out. So, I trimmed my script to minimal basic and it still gives me same error. > mydata <- ReadAffy() > esetRMA <- rma(mydata) Background correcting Normalizing Calculating Expression > esetRMA ExpressionSet (storageMode: lockedEnvironment) assayData: 45101 features, 12 samples element names: exprs protocolData sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: mouse4302 > sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4') > group <-factor(sampletype) > design<- model.matrix(~0+group) > colnames(design) <- c('WB','Ten','Eleven','Twelve') > fit <- lmFit(esetRMA, design) > contrast.matrix<-makeContrasts(Ten-WB, levels=design) > fit2<- contrasts.fit(fit,contrast.matrix) > fit2 <- ebayes(fit2) > topTable(fit2, adjust = "fdr", number = 50) Error in 1:ncol(fit) : argument of length 0 > topTable(fit2,coef = 1, adjust = "fdr", number = 50) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type > results <- decideTests(fit2) Error in decideTests(fit2) : Need MArrayLM object Could anybody please explain me or point out what I am missing here? Its strange that I wrote a similar script for Illumina which works just fine. AK -- Atul Kakrana Delaware Technology Park

Dear Atul, You have uses ebayes() when you intended eBayes(). Best wishes Gordon > Date: Thu, 04 Apr 2013 19:01:24 -0400 > From: Atul Kakrana <atulkakrana at="" gmail.com=""> > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] Limma - Result output - Error - Help > Message-ID: <515E0644.9050304 at gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hello All, > > I wrote a script to analyse affymetrix data but its giving an error > while using the topTable from limma: > > Error in array(x, c(length(x), 1L), if (!is.null(names(x))) > list(names(x), : > 'data' must be of a vector type > > I checked all the steps that might be causing the error but couldn't > find out. So, I trimmed my script to minimal basic and it still gives me > same error. > >> mydata <- ReadAffy() >> esetRMA <- rma(mydata) > Background correcting > Normalizing > Calculating Expression >> esetRMA > ExpressionSet (storageMode: lockedEnvironment) > assayData: 45101 features, 12 samples > element names: exprs > protocolData > sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total) > varLabels: ScanDate > varMetadata: labelDescription > phenoData > sampleNames: 00.0A.CEL 00.0B.CEL ... 12.5C.CEL (12 total) > varLabels: sample > varMetadata: labelDescription > featureData: none > experimentData: use 'experimentData(object)' > Annotation: mouse4302 >> sampletype <- c('1','1','1','2','2','2','3','3','3','4','4','4') >> group <-factor(sampletype) >> design<- model.matrix(~0+group) >> colnames(design) <- c('WB','Ten','Eleven','Twelve') >> fit <- lmFit(esetRMA, design) >> contrast.matrix<-makeContrasts(Ten-WB, levels=design) >> fit2<- contrasts.fit(fit,contrast.matrix) >> fit2 <- ebayes(fit2) > >> topTable(fit2, adjust = "fdr", number = 50) > Error in 1:ncol(fit) : argument of length 0 > >> topTable(fit2,coef = 1, adjust = "fdr", number = 50) > Error in array(x, c(length(x), 1L), if (!is.null(names(x))) > list(names(x), : > 'data' must be of a vector type > >> results <- decideTests(fit2) > Error in decideTests(fit2) : Need MArrayLM object > > > Could anybody please explain me or point out what I am missing here? Its > strange that I wrote a similar script for Illumina which works just fine. > > AK > > -- > Atul Kakrana > Delaware Technology Park > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}