Hello Davis,
I did run estimateCommonDisp() and then estimageTagwiseDisp(). AND also did
the following codes:

> dt06 <- estimateTagwiseDisp(d06, prior.n = 10)
> names(dt06)
> head(dt06$tagwise.dispersion)
[1] 0.6054731 0.5433415 0.5083185 0.6054731 0.5553801 0.4640211
> summary(dt06$tagwise.dispersion)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
 0.4122  0.4223  0.4428  0.4613  0.4748  1.1390
> d06$common.dispersion
[1] 0.4588705
> prior.n06 <- estimateSmoothing(d06)
> prior.n06
[1] 5.131239e-05

When I tried to run exactTest, I am getting the following error message:
> de.tagwise06 <- exactTest(d06, common.disp = FALSE)
Comparison of groups:  PPLB6dpi - PhyP18
Error in q2qnbinom(object$counts, input.mean = input.mean, output.mean =
output.mean,  :
  dims [product 49700] do not match the length of object [0]

I am curious what does it mean by "do not match the length of object[0]"?
How this error can be fixed?

Many thanks!
Sridhara



On Thu, Mar 3, 2011 at 9:26 PM, Sridhara Gupta Kunjeti <sridhara@udel.edu>wrote:

> 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
>> ------------------------------
>>
>>
>> ______________________________________________________________________
>> The information in this email is confidential and intended solely for the
>> addressee.
>> You must not disclose, forward, print or use it without the permission of
>> the sender.
>> ______________________________________________________________________
>>
>
>
>
> --
> Sridhara G Kunjeti
> PhD Candidate
> University of Delaware
> Department of Plant and Soil Science
> email- sridhara@udel.edu
> Ph: 832-566-0011
>



-- 
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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