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Old 07-16-2014, 01:16 PM   #1
KYR
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Location: Toronto

Join Date: May 2012
Posts: 18
Exclamation DESeq2 - COLUMN and ROWS number don't match

I have a table of count of control (3 replicates), treatment B (3 replicates) and treatment A (3 replicates). The first column is the gene symbol, table is as below:

Gene_symbol C1 C2 C3 B1 B2 B3 A1 A2 A3

Code:
library( "DESeq2" )
library("Biobase")
mydata = read.table("matrix4.txt", header=TRUE)
samples <- data.frame(row.names=c("C1", "C2", "C3", "B1", "B2", "B3", "A1", "A2", "A3"), condition=as.factor(c(rep("C",3), rep("B", 3), rep("A", 3))))

dds <- DESeqDataSetFromMatrix(countData = as.matrix(mydata), colData=samples, design=~condition)

Error in validObject(.Object) : 
  invalid class “SummarizedExperiment” object: 'colData' nrow differs from 'assays' ncol
How can I point to DESeq2 that gene symbol isn't row.data ?
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Old 07-16-2014, 01:21 PM   #2
Michael Love
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Default

you've posted 3 times now about the same example, can we keep all the discussion on a single thread for simplicity?

indeed Devon Ryan's answer 10 minutes before this post is the correct one.

http://seqanswers.com/forums/showthread.php?t=45029
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