User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey330
Reputation:
330
Status:
Trusted
Location:
Johns Hopkins University, Baltimore, USA
Website:
http://www.peterhickey...
Twitter:
PeteHaitch
Scholar ID:
Google Scholar Page
Last seen:
2 weeks ago
Joined:
5 years, 5 months ago
Email:
p***********@gmail.com

Posts by Peter Hickey

<prev • 67 results • page 1 of 7 • next >
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Answer: A: how to combine multiple DelayedArray to a high dimension array
... There's no general abind() method for DelayedArray at this time. However, for your particular example, you can achieve it with some trickery using aperm() with arbind(): suppressPackageStartupMessages(library(DelayedArray)) # NOTE: I add a 4th dimension to the array a <- array(runif(1500000), ...
written 4 weeks ago by Peter Hickey330
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Comment: C: Finding DMRs using dmrFinder in bsseq
... Please post your question separately rather than as a comment on an existing question. Your questions are very broad and I don't full understand where exactly you need help. Please read the posting guide so that others can help you more easily. ...
written 5 weeks ago by Peter Hickey330
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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 4 months ago by Peter Hickey330
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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 5 months ago by Peter Hickey330
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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 5 months ago by Peter Hickey330
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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 5 months ago by Peter Hickey330
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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 5 months ago by Peter Hickey330
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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 6 months ago by Peter Hickey330
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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 6 months ago by Peter Hickey330
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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 9 months ago by Peter Hickey330

Latest awards to Peter Hickey

Scholar 10 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.2 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.2 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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