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

[Laurent Gautier]

On 1/3/11 6:45 PM, kristen.dang at syngenta.com wrote:
> 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?

The build bots have not done it yet (at least they did not when I 
checked). You can fetch it from the code repository/

svn --username readonly --password readonly co 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/edgeR



L.
> 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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