Hello,

I have a matrix with column names. When creating a DESeqDataSet, the resulting 
matrix has changed column names to numbers. This causes problems if trying to 
create an ExpressionSet with it, for example, after regularised logarithm 
transformation, because the sample names no longer agree.

exprMatrix <- matrix(c(rnbinom(50, 1/0.15, mu = 30), rnbinom(50, 1/0.15, mu = 
10)), ncol = 10)
colnames(exprMatrix) <- LETTERS[1:10]
exampleDDS <- DESeqDataSetFromMatrix(exprMatrix, data.frame(class = 
rep(c("Poor", "Good"), each = 5)), formula(~ class))

groupsTable <- data.frame(class = rep(c("Poor", "Good"), each = 5))
rownames(groupsTable) <- LETTERS[1:10]
exampleSet <- ExpressionSet(counts(exampleDDS), AnnotatedDataFrame(groupsTable))
Error in validObject(.Object) : 
  invalid class “ExpressionSet” object: 1: sampleNames differ between assayData 
and phenoData
invalid class “ExpressionSet” object: 2: sampleNames differ between phenoData 
and protocolData

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia

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