Hello Davis and Mark,
Thank you very much for your response!
I will run first common dispersion and then tagwise dispersion.

Many thanks!
Sridhara


On Thu, Mar 3, 2011 at 9:20 PM, Mark Robinson <mrobinson@wehi.edu.au> wrote:

> Hi Sridhara.
>
> You do need to run estimateCommonDisp() before estimateTagwiseDisp().
>  We've modified the code now to detect whether it has been run and if not,
> invisibly call it.
>
> Mark
>
> On 2011-03-04, at 1:03 PM, Sridhara Gupta Kunjeti wrote:
>
> > 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
> >
> >       [[alternative HTML version deleted]]
> >
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>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: mrobinson@wehi.edu.au
> e: m.robinson@garvan.org.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
>
>
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