[Bioc-devel] DESeqDataSetFromMatrix Changes Column Names

[Michael Love]

Hi Dario,

Which version are you using?

I think the column names of the matrices in the assays of
SummarizedExperiment are coming from the rownames of colData.

My priority is to avoid doubling the memory footprint in object creation. I
think preserving the colnames of the matrix was relevant to memory usage at
some point, but I forget exactly the details.

Mike
On Aug 25, 2014 10:35 PM, "Dario Strbenac" <dstr7320 at uni.sydney.edu.au>
wrote:

> 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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