Error in Apeglm Method for Effect Size Shrinkage
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rbenel ▴ 20
@rbenel-13642
Last seen 6 days ago
Israel

Hi, 

I have been trying to utilize apeglm for shrinking , and I am receiving the error message below; however, normal works just fine...I am using DESeq2_1.18.1 and apeglm_1.0.3.

resLFC <- lfcShrink(dds, coef="condition_treated_vs_untreated", type="apeglm")

using 'apeglm' for LFC shrinkage
Error in solve.default(o$hessian) :
  system is computationally singular: reciprocal condition number = 1.36798e-116

deseq2 apeglm • 426 views
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@mikelove
Last seen 6 hours ago
United States

Thanks for the report.

It could be that apeglm is just having a hard time chugging away at the GLM. Out of curiosity what is dim(model.matrix(design(dds), colData(dds)))?

I'd recommend using type="ashr", if you wanted shrunken LFC and "apeglm" can't fit. ashr doesn't need to working with the design matrix, because it models the coefficients and standard errors from DESeq2 alone.

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Hi Michael, 

Here are the dimension of the model:

dim(model.matrix(design(dds), colData(dds)))
[1] 32 13

type = "ashr" gives me this type of warning message: 

Due to absence of package REBayes, switching to EM algorithm

I have tried to install the REBayes package, but I am currently having issues installing the package because it is dependent on

Rmosek which requires mosek on the local machine and the mosek installation is giving me issues.....

Update: I successfully installed all of the dependencies, and now type = "ashr" is working.

 

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Sorry just got to this. The message above is not an error. You can also use ashr with the EM algorithm which happens if it can’t find this other package (although I suppose the REBayes is preferred and we have installed this on our cluster).

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OK. I successfully installed REBayes, but users should know that it has dependencies to Rmosek, which requires instillation of mosek to one's local computer, which requires a license... so it was a bit of a long process to install the REBayes package. 

Thanks!

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