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Old 07-21-2011, 03:09 AM   #3
dariober
Senior Member
 
Location: Cambridge, UK

Join Date: May 2010
Posts: 311
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Hi,
I think the problem is in the count table (over). In your case the first column contains the gene name instead of containing the first count. You should be able to fix it by removing the first column and by assigning gene names to row names (untested):
Code:
over <- read.delim("C:\\Nandan\\TagSeqExample_top.tab", header=TRUE, stringsAsFactors=TRUE)
gene_names<- over[,1]
over<- over[,2:ncol(over)]
rownames(over)<- gene_names
## ...etc
Also, I don't remember the functions of DESeq exactly but I think the vector of conditions should be of the same length as the the number of samples so your conds=c(rep("GZ", 1), rep("DZ", 1)) is incorrect.

Dario
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