Question: How do I prevent my R kernel (Jupyter Notebook) from dying after running variance stabilizing transformation?
0
gravatar for david.wheeler7
7 months ago by
david.wheeler720 wrote:

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

deseq2 • 196 views
ADD COMMENTlink modified 7 months ago by Michael Love25k • written 7 months ago by david.wheeler720
Answer: How do I prevent my R kernel (Jupyter Notebook) from dying after running varianc
0
gravatar for Michael Love
7 months ago by
Michael Love25k
United States
Michael Love25k wrote:

No idea. This has never happened to me, and so I'd guess it's not a DESeq2 issue.

How many samples is dds? Do you have some very small memory available?

ADD COMMENTlink written 7 months ago by Michael Love25k

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!

ADD REPLYlink written 7 months ago by david.wheeler720

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.

ADD REPLYlink written 7 months ago by Michael Love25k

I just tried the same code in R proper, straight from the console.

This was the output:

> vsd <- vst(dds, blind = FALSE)

*** 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:

ADD REPLYlink written 7 months ago by david.wheeler720

I think there’s an issue with your installation. Sorry I don’t have any idea because I’ve never seen this.

ADD REPLYlink written 7 months ago by Michael Love25k

Can you check BiocManager::valid()?

ADD REPLYlink modified 7 months ago • written 7 months ago by Michael Love25k
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