User: Peter Hickey

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Peter Hickey380
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Johns Hopkins University, Baltimore, USA
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http://www.peterhickey...
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PeteHaitch
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Posts by Peter Hickey

<prev • 78 results • page 1 of 8 • next >
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Comment: C: Minfi error when using force=TRUE in read.metharray
... I believe this is cross-posted from https://github.com/hansenlab/minfi/issues/173. Based on the sessionInfo() you posted there, you are using an old version of minfi. As recommended in http://www.bioconductor.org/help/support/posting-guide/, please try updating to the latest version (see http://www. ...
written 4 days ago by Peter Hickey380
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Comment: C: Minfi error when using force=TRUE in read.metharray
... Please include the output of sessionInfo() otherwise we don't know what version of R or minfi you are using. Please also read http://www.bioconductor.org/help/support/posting-guide/ for advice on creating a question that will be easier for people to help you answer. ...
written 4 days ago by Peter Hickey380
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Comment: C: Installation of package DelayedArray had non-zero exit status
... To clarify, was this using BiocInstaller::biocLite("DelayedArray")? ...
written 22 days ago by Peter Hickey380
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Answer: A: How to obtain summary statistics for all Bioc releases
... Sharing my reply to Robert's email; he asked for the data behind a post I wrote that included a graph of number of packages per release (http://blog.revolutionanalytics.com/2015/08/a-short-introduction-to-bioconductor.html). The post is from a few releases back, but I've updated the code. The data ...
written 11 weeks ago by Peter Hickey380
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Comment: C: Help using 'handler' function with bptry()
... Very good point re not clobbering result if invoked with se <- f(se, ...). Hmm, there are more dragons here than I'd initially considered. I'll keep thinking on this (it may be more trouble than it's worth). Thanks for your advice, Martin. ...
written 11 weeks ago by Peter Hickey380
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Comment: C: Help using 'handler' function with bptry()
... Perhaps I need to think about this more. The design I had in mind is as follows. f(): A user-level function that takes a SummarizedExperiment. It breaks up the assay-data into chunks and uses BiocParallel to process these chunks in parallel. Finally, it constructs a new assay from these outputs tha ...
written 11 weeks ago by Peter Hickey380
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Help using 'handler' function with bptry()
... In a long-running function I am writing, I use bptry() around bplapply() so that I might re-do failed tasks (this is such a cool feature!). If any failures are detected, I want to return a custom error message to help the user re-run just the failed tasks, along with the partial results. Right now, ...
biocparallel error handling written 12 weeks ago by Peter Hickey380 • updated 11 weeks ago by Martin Morgan ♦♦ 22k
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Answer: A: Request to remove requirement for gr to have widths 1 in BSseq constructor
... That seems a reasonable request, Raymond. Let's continue the discussion on the GitHub issue (I prefer that for more code-focused issues).  ...
written 3 months ago by Peter Hickey380
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Comment: C: Strange error in bsseq when trying to assign seqinfo
... Thanks for the detailed bug report, @rcavalca. I can confirm that running 2B in a clean session leads to the error. However, it's not an issue with bsseq but rather something else, perhaps in SummarizedExpeirment. On BioC 3.7: seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19') se <- Summarize ...
written 3 months ago by Peter Hickey380
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Comment: C: Dependency installation error due to no longer available CRAN packages ('rngtool
... I was unable to replicate this on a Linux machine using Bioconductor 3.7. Neither 'rngtools' or 'pkgmaker' appears to be archived on CRAN (as of 2018-05-14), although the CRAN check pages do indicate some errors on linux with r-devel, r-patched, and r-release (https://cran.r-project.org/web/checks/ ...
written 3 months ago by Peter Hickey380

Latest awards to Peter Hickey

Popular Question 3 months ago, created a question with more than 1,000 views. For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
Scholar 3 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: From RleList to RleArray
Scholar 13 months ago, created an answer that has been accepted. For A: About methylation data processing
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Error when generate mapToGenome
Scholar 13 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Popular Question 13 months ago, created a question with more than 1,000 views. For Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
Popular Question 13 months ago, created a question with more than 1,000 views. For Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
Scholar 14 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.5 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.5 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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