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Old 07-16-2014, 07:35 AM   #2
Michael Love
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Location: Boston

Join Date: Jul 2013
Posts: 333
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This is your countData, which has as many rows as genes:

Code:
mydata = read.table("matrix.txt", header=TRUE)
col1 <- mydata[,1]
It looks like this will be the colData (sample information table).

Code:
ExpDesign = data.frame(row.names=col1, condition=c("C", "C", "C", "A", "A", "A", "B", "B", "B")
...which has as many rows as samples.

So the error comes when you try to name the rows of your colData using the gene names in col1.

You will also get an error later when you try to run
Code:
assay( mydata )
because mydata is a data.frame. assay() is a function for getting a matrix from SummarizedExperiment objects. You can just use
Code:
as.matrix( mydata )
in order to supply a matrix to DESeqDataSet.
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