View Single Post
Old 07-16-2014, 12:15 PM   #1
KYR
Member
 
Location: Toronto

Join Date: May 2012
Posts: 18
Exclamation Need help with DESeq2

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

[Gene Symbol] [C1] [C2] [C3] [B1] [B2] [B3] [A1] [A2] [A3]
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")
mydata4 = read.table("matrix4.txt", header=TRUE)
head(mydata4)

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))))
Error in data.frame(row.names = c("C1", "C2", "C3", "B1", "B2", "B3",  : 
  row names supplied are of the wrong length

How can I fix that ? I seems I need to subset my data though I don't know how to do this and deseq2 doesn't transpose my columns to rows
KYR is offline   Reply With Quote