[BioC] edgeR - tagwise dispersion

[Mark Robinson]

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 at udel.edu
> Ph: 832-566-0011
> 
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> 
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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