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david.wheeler7
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@davidwheeler7-19959
Last seen 5.2 years ago
Hello!
I am following this vignette: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html.
Everytime I run the below code to stabilize the variance:
vsd <- vst(dds, blind = FALSE)
I receive this message:
"Kernel Restarting The kernel appears to have died. It will restart automatically"
Has anyone encountered this before and found a solution?
Thank you for your time!
David
Samples = 9, transcripts = 246300.
I am not sure what constitutes small here. This is what I have: 16 GB | 2 memory slots, each of which accepts a 2400 MHz DDR4 memory module.
Is that too small?
Thanks again!
That's fine, I never know if people have 9 samples or 9,000.
I don't think this is a DESeq2 issue. I've never had such a problem using vst() in R.
I just tried the same code in R proper, straight from the console.
This was the output:
*** caught segfault *** address 0x18, cause 'memory not mapped'Traceback:1: fitDisp(ySEXP = ySEXP, xSEXP = xSEXP, mu_hatSEXP = mu_hatSEXP, log_alphaSEXP = log_alphaSEXP, log_alpha_prior_meanSEXP = log_alpha_prior_meanSEXP, log_alpha_prior_sigmasqSEXP = log_alpha_prior_sigmasqSEXP, min_log_alphaSEXP = min_log_alphaSEXP, kappa_0SEXP = kappa_0SEXP, tolSEXP = tolSEXP, maxitSEXP = maxitSEXP, usePriorSEXP = usePriorSEXP, weightsSEXP = weightsSEXP, useWeightsSEXP = useWeightsSEXP)2: fitDispWrapper(ySEXP = counts(objectNZ)[fitidx, , drop = FALSE], xSEXP = modelMatrix, mu_hatSEXP = fitMu, log_alphaSEXP = log(alpha_hat)[fitidx], log_alpha_prior_meanSEXP = log(alpha_hat)[fitidx], log_alpha_prior_sigmasqSEXP = 1, min_log_alphaSEXP = log(minDisp/10), kappa_0SEXP = kappa_0, tolSEXP = dispTol, maxitSEXP = maxit, usePriorSEXP = FALSE, weightsSEXP = weights, useWeightsSEXP = useWeights) 3: estimateDispersionsGeneEst(object.sub, quiet = TRUE) 4: vst(dds, blind = FALSE)Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection:I think there’s an issue with your installation. Sorry I don’t have any idea because I’ve never seen this.
Can you check BiocManager::valid()?