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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