User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey320
Reputation:
320
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Trusted
Location:
Johns Hopkins University, Baltimore, USA
Website:
http://www.peterhickey...
Twitter:
PeteHaitch
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Google Scholar Page
Last seen:
1 week, 5 days ago
Joined:
5 years, 2 months ago
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Posts by Peter Hickey

<prev • 65 results • page 1 of 7 • next >
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Answer: A: Error when generate mapToGenome
... Thank you for including the code and sessionInfo() in your question, which makes it easy to help you. Based on your sessionInfo(), you are mixing packages from different Bioconductor versions: minfi, minfiData, IlluminaHumanMethylation450kanno.ilmn12.hg19, and IlluminaHumanMethylation450kmanifest a ...
written 7 weeks ago by Peter Hickey320
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Comment: C: From RleList to RleArray
... Will try to write a PR to add this to DelayedArray over the next few days ...
written 10 weeks ago by Peter Hickey320
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Answer: A: From RleList to RleArray
... rm <- RleArray(unlist(rl), c(lengths(rl)[1], length(rl))) will give you what you want (the unlist() is cheap because of how an RleList is defined). With some checks added, this could become the as(rl, "RleArray") method. ...
written 10 weeks ago by Peter Hickey320
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Comment: C: BSmooth 'names' attribute must be the same length as the vector
... Yes, it does sound a little odd. Especially since you have unstranded CpGs (my guess based on having 58,165,645 rows = 2 * 24 million CpGs in hg19) ...
written 12 weeks ago by Peter Hickey320
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Comment: C: BSmooth 'names' attribute must be the same length as the vector
... That does sound unusual; smoothing is memory intensive but shouldn't be that bad. This is CpG methylation, correct? And you're running it with Meth.cov.fit <- BSmooth(Meth.cov, mc.cores = 32, verbose = TRUE)? ...
written 12 weeks ago by Peter Hickey320
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Answer: A: BSmooth 'names' attribute must be the same length as the vector
... Hi Ravi, I have seen this error before when running on a cluster with a large value of mc.cores. Unfortunately, I don't know the exact cause (I suspect one of the jobs dies, possibly because it runs out of memory). I have been able to get around this by reducing to, say, mc.cores = 8. Does this wor ...
written 3 months ago by Peter Hickey320
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Comment: C: Error from scater package
... Please include the output of sessionInfo() in your question (http://www.bioconductor.org/help/support/posting-guide/) ...
written 3 months ago by Peter Hickey320
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Answer: A: Unusually long running times for getMeth function since latest release
... Thanks for your patience, Alejandro. I've committed a fix - it's available from https://github.com/PeteHaitch/bsseq. If you're able to, would you please give it a try to confirm that it fixes the performance regression. It requires that you are using Bioc-devel and can then be installed with BiocIns ...
written 6 months ago by Peter Hickey320
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Comment: C: Unusually long running times for getMeth function since latest release
... Hi Alejandro, Reproducible code and data would be appreciated. No need for it to be the full object, just enough for issue to be a noticeable drag on performance. Cheers, Pete On Fri., 30 Jun. 2017, 9:37 am Alejandro Reyes [bioc], < noreply@bioconductor.org> wrote: > Activity on a post ...
written 6 months ago by Peter Hickey320
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Comment: C: Unusually long running times for getMeth function since latest release
... I noticed this too but haven't had time to fix. I have an inkling of what's causing this and I'll try to fix over the weekend On Thu., 29 Jun. 2017, 5:48 pm Kasper Daniel Hansen [bioc], < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org & ...
written 6 months ago by Peter Hickey320

Latest awards to Peter Hickey

Scholar 7 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 23 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 23 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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