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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
