[BioC] edgeR - tagwise dispersion

[Mark Robinson]

Maybe you've made a typo?  How about trying:

de.tagwise06 <- exactTest(dt06, common.disp = FALSE)

... since the 'd06' object doesn't have the tagwise dispersions.

Also, when you report errors, it's handy to also give the output of traceback() and sessionInfo().  No need in this case, of course.

Cheers,
Mark


On 2011-03-04, at 1:43 PM, Sridhara Gupta Kunjeti wrote:

> 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 at 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 at 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 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
> ------------------------------
> 
> 
> ______________________________________________________________________
> 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 at udel.edu
> Ph: 832-566-0011
> 
> 
> 
> -- 
> Sridhara G Kunjeti
> PhD Candidate
> University of Delaware
> Department of Plant and Soil Science
> email- sridhara at udel.edu
> Ph: 832-566-0011

------------------------------
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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