[BioC] EdgeR - problems running estimateCRDisp
mailinglist.honeypot at gmail.com
Fri Oct 22 14:10:57 CEST 2010
I'm going to cut out most of your email to highlight the relevant part:
On Fri, Oct 22, 2010 at 1:44 AM, <josquin.tibbits at dpi.vic.gov.au> wrote:
> I am running the new EdgeR package 1.8 and have updated R to 1.12.0 and
> updated all the packages I have installed.
> I have an RNAseq experiment with 24 samples and am wanting to run a glm
> analysis using the Cox-Reid common dispersion (and tagwise) paramaters.
> DGEList.object <- estimateCRDisp(DGEList.object, design)
> This step is giving the following error:::
> Loading required package: MASS
> Error: NA/NaN/Inf in foreign function call (arg 1)
> In addition: Warning messages:
> 1: glm.fit: algorithm did not converge
> 2: step size truncated due to divergence
>  "samples" "counts"
> Clearly the function is not working. I have tried two different computers
> and a run it in 64 bit but always with the same result.
Perhaps this is too simple a suggestion on my part, but do you have
any "such" values in your DGEList.object$counts matrix? And by "such"
I mean NA, NaN, or Inf values for some counts?
What does range(DGEList.object$counts) give you?
There's another description from the R-help archives of why this might
also happen, but I'm not sure how helpful that is to you at the
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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