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Old 07-15-2014, 10:55 PM   #1
KYR
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Location: Toronto

Join Date: May 2012
Posts: 18
Exclamation DESeq2 error in data.frame (multiple treatments and multiple replicates)

I have a text file, containing read counts per gene for each treatments and control, with the following column

[Gene Symbol] [C1] [C2] [C3] [A1] [A2] [A3] [B1] [B2] [B3]
  • C is Control
  • A is Treatment 1
  • B is Treatment 2
-> Each of C, A an B have 3 replicates

When I do data.frame it generates an error

Code:
library( "DESeq2" )
library("Biobase")
mydata = read.table("matrix.txt", header=TRUE)
col1 <- mydata[,1]

## Error message
ExpDesign = data.frame(row.names=col1, condition=c("C", "C", "C", "A", "A", "A", "B", "B", "B")
Error in data.frame(row.names = col1, condition = c("C", "C", "C", "A",  : 
  row names supplied are of the wrong length
## The following is what I would next if I didn't have any error message
Code:
countdata <- assay( mydata )
head( countdata )
coldata <- colData( mydata )
rownames( coldata ) <- coldata$run
colnames( countdata ) <- coldata$run
head( coldata[ , c("C", "C", "C", "A", "A", "A", "B", "B", "B") ] )
Eventually the goal is to have a heatmap with each replicates in the control, treatment A and B.

I think the problem comes from the fact that I should subset my data, though I have no clue how to do to that. Any suggestions on where is the error message coming from and how to subset data? (If I should ever subset that..)

Last edited by KYR; 07-15-2014 at 10:57 PM. Reason: typo
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Old 07-16-2014, 06:35 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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