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