Error In Lumitx.lumi Slot Se.exprs Is Required
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8.1 years ago by Sharon Anbu • 470 Sharon Anbu • 470 wrote: Hi,
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Since my datafile is not in a standard format, I am usb vid trying to create a new lumi object with following information: AVG_Signal, Detection.Pval, Avg_NBEADS and BEAD_STDERR. I lumi package 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]] ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 8.1 years ago by Pan Du • 1.2k • written 8.1 years ago by Sharon Anbu • 470 0 8.1 years ago by Pan Du • 1.2k Pan Du • 1.2k wrote: 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"
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