[Bioc-sig-seq] error msg from edgeR estimateCRDisp

[Wong, Chao-Jen]

Hi, Kristen,

You can find the newest version of edgeR here:

http://bioconductor.org/help/bioc-views/2.8/bioc/html/edgeR.html

You can either manually install edgeR 2.1.4 or use the biocLite function if you are using R 2.13.

Chao-Jen
----- Original Message -----
From: "kristen dang" <kristen.dang at syngenta.com>
To: smyth at wehi.EDU.AU
Cc: laurent at cbs.dtu.dk, bioc-sig-sequencing at r-project.org
Sent: Monday, January 3, 2011 9:45:51 AM
Subject: [Bioc-sig-seq] error msg from edgeR estimateCRDisp

Dear Gordon,
Many thanks for your reply.

I apologize, but I cannot find where to download version 2.0.3 of edgeR. I can only find 2.0.2 on the bioconductor site. Would you point me to the appropriate location?

Thank you for suggesting the rounding -- I had forgotten that the count data provided to me included decimals. However, after adding the rounding, I get a new error from the estimateCRDisp function:

> data = readDGE(targets)
> data$counts = round(data$counts)
> data = calcNormFactors(data)
> contrasts(targets$factor_a) = contr.sum(2)
> contrasts(targets$factor_b) = contr.sum(2)
> design = model.matrix(~factor_a + factor_b, data = targets)
> data.cd = estimateCRDisp(data, design)
Error in chol.default(crossprod(design, .vecmat(mu[i, ]/(1 + dispersion *  :
  the leading minor of order 4 is not positive definite

> traceback()
5: .Call("La_chol", as.matrix(x), PACKAGE = "base")
4: chol.default(crossprod(design, .vecmat(mu[i, ]/(1 + dispersion *
       mu[i, ]), design)))
3: chol(crossprod(design, .vecmat(mu[i, ]/(1 + dispersion * mu[i,
       ]), design)))
2: adjustedProfileLik(spline.disp[i], y.filt, design = design, offset = offset.mat.filt +
       lib.size.mat.filt)
1: estimateCRDisp(data, design)
>

Any suggestions are much appreciated.

Regards,
Kristen Dang



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-- 
Chao-Jen Wong 
Program in Computational Biology 
Division of Public Health Sciences 
Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2 at fhcrc.org