Hi,
I am using edgeR for DGE analysis and I have two samples with two
replication.

I was successful in passing through the following codes
> setwd("C:/Users/SRIDHARA/Documents/Sequence analysis/02-Pphaseoli")
> targets <- read.delim(file = "targets.txt", stringsAsFactors = FALSE)
> targets <- read.delim(file = "targetsF0P6.txt", stringsAsFactors = FALSE)
> targets
> d <- readDGE(targets, header = FALSE)
> d

and then when I used TagWisedispersion, I get the following error message
> d <- estimateTagwiseDisp(d, prior.n = 10)
Error in t.default(object$counts) : argument is not a matrix

I was not sure, if I need to do
> d <- estimateCommonDisp(d)
AND then
> d <- estimateTagwiseDisp(d, prior.n = 10)
if I do this way, I do not get any error message. BUT I think, TagwiseDisp
should work without calculating CommonDisp.
Any suggestions will be highly appreciated.

Thanks,
Sridhara

-- 
Sridhara G Kunjeti
PhD Candidate
University of Delaware
Department of Plant and Soil Science
email- sridhara@udel.edu
Ph: 832-566-0011

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