Hi, Since my datafile is not in a standard format, I am trying to create a new lumi object with following information: AVG_Signal, Detection.Pval, Avg_NBEADS and BEAD_STDERR. I have used, require(lumi) dat.lumi <- new('LumiBatch', exprs = as.matrix(signalRaw), se.exprs = as.matrix(std), beadNum = as.matrix(nb), detection = as.matrix(detP) ) I am getting: Error in validObject(.Object) : invalid class "LumiBatch" object: sampleNames differ between assayData and phenoData > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.6.2 mgcv_1.4-0 affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 Am I doing anything wrong? Thanks in advance. Best regards, Sharon [[alternative HTML version deleted]]

Hi Sharon, You should make each element of AssayData slot have the same row names and column names. Here is an example of creating new LumiBatch object. The exprs and se.exprs are required, others are optional. library(lumi) data(example.lumi) newLumi = new('LumiBatch', exprs=exprs(example.lumi), se.exprs=se.exprs(example.lumi), detection=detection(example.lumi), beadNum=beadNum(example.lumi)) Pan On 8/27/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 6 > Date: Tue, 26 Aug 2008 16:38:13 +0100 > From: Sharon <sharonanandhi at="" gmail.com=""> > Subject: [BioC] LumiBatch - Error in creating lumi object > To: bioconductor at stat.math.ethz.ch > Message-ID: > <3709c2370808260838s59061dc7kcdc46908b9139fe2 at mail.gmail.com> > Content-Type: text/plain > > Hi, > > Since my datafile is not in a standard format, I am trying to create a new > lumi object with following information: AVG_Signal, Detection.Pval, > Avg_NBEADS and BEAD_STDERR. I have used, > > require(lumi) > dat.lumi <- new('LumiBatch', exprs = as.matrix(signalRaw), se.exprs = > as.matrix(std), beadNum = as.matrix(nb), detection = as.matrix(detP) ) > > I am getting: > > Error in validObject(.Object) : > invalid class "LumiBatch" object: sampleNames differ between assayData and > phenoData > >> sessionInfo() > R version 2.7.1 (2008-06-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] lumi_1.6.2 mgcv_1.4-0 affy_1.18.2 > preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 > > Am I doing anything wrong? > > Thanks in advance. > > Best regards, > Sharon > > [[alternative HTML version deleted]] > >