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Old 07-16-2014, 12:59 PM   #3
Location: Toronto

Join Date: May 2012
Posts: 18

Originally Posted by dpryan View Post
That command won't produce the error you showed.
Indeed, I started again from a fresh R command shell, and that error doesn't appear anymore. However it generates another one:

library( "DESeq2" )
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

So I check the number of columns and rows for each and ncol has 1 more than ncol

I'm guessing it's coming from the gene symbol column..though how can I fix this??

Last edited by KYR; 07-16-2014 at 01:11 PM. Reason: typo
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