[BioC] edgeR - tagwise dispersion

[Davis McCarthy]

Hi Sridhara

Thanks for reporting this bug - it is a known issue (and indeed resolved in the devel version of edgeR). 

The expected edgeR pipeline has been for the user to call estimateCommonDisp() first, then call estimateTagwiseDisp() subsequently if desired. The reason for this is that to estimate tagwise dispersions we require results computed by estimateCommonDisp(). 

However, it is certainly reasonable to expect estimateTagwiseDisp() to run even if estimateCommonDisp() has not been run - this has been changed in the current devel version of edgeR on Bioconductor. With this change, estimateTagwiseDisp() will internally call estimateCommonDisp() if it detects that estimateCommonDisp() has not already been run on the DGEList object. In terms of computation time there is no difference whether you call estimateCommonDisp() before estimateTagwiseDisp() or not.

The common  dispersion does provide information about the overall extent of difference between replicate libraries, so personally I like to have a look at this value whenever carrying out an analysis, before going on to use the tagwise dispersions.

For your purpose, either run estimateCommonDisp() before estimateTagwiseDisp() with the release version, or get hold of the devel version.

Best regards
Davis



On Mar 4, 2011, 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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------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au



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