[BioC] edgeR - tagwise dispersion

Mark Robinson mrobinson at wehi.EDU.AU
Fri Mar 4 03:20:55 CET 2011


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
> 
> 	[[alternative HTML version deleted]]
> 
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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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