User: Peter Hickey

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Peter Hickey380
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Location:
Johns Hopkins University, Baltimore, USA
Website:
http://www.peterhickey...
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PeteHaitch
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9 hours ago
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Posts by Peter Hickey

<prev • 83 results • page 1 of 9 • next >
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Why is it beneficial to store the data as a single Rle in SolidRleArraySeed? I think it's more the case that this is a simpler object to design and program with (Hervé Pagès will know best). Doesn't that limit to the total size of the matrix since it spans all columns? Yes, I think so. If yo ...
written 9 hours ago by Peter Hickey380
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... suppressPackageStartupMessages(library(S4Vectors)) suppressPackageStartupMessages(library(DelayedArray)) nrow <- 200L ncol <- 5L # Generate some data that can be efficiently run length encoded. x <- Rle(500L + sort(rpois(nrow * ncol, 10))) x #> integer-Rle of length 1000 with 21 runs # ...
written 16 hours ago by Peter Hickey380
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Answer: A: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... I'm going to assume we're talking about representing 2-dimesionsal arrays. It comes down to how the data are stored (i.e. run length encoded): A DataFrame with Rle columns is run length encoded column-wise with a separate Rle per column. A SolidRleArraySeed-backed DelayedArray is run length enc ...
written 16 hours ago by Peter Hickey380
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Comment: C: Recommendations for combining multiple 10x runs into one SingleCellExperiment
... Thanks, Aaron. Very helpful (as always). ...
written 4 days ago by Peter Hickey380
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Recommendations for combining multiple 10x runs into one SingleCellExperiment
... I've got an experiment with eight 10x scRNA-seq runs that I'm analysing by starting with something based on the simpleSingleCell workflow. I constructed each SingleCellExperiment with DropletUtils::read10xCounts(). I'm looking for any opinions or advice on when to combine these into one SingleCellE ...
simplesinglecell singlecellexperiment dropletutils written 7 days ago by Peter Hickey380 • updated 7 days ago by Aaron Lun21k
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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 10 weeks 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 10 weeks 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 12 weeks 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 4 months 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 4 months ago by Peter Hickey380

Latest awards to Peter Hickey

Popular Question 5 months ago, created a question with more than 1,000 views. For VariantAnnotation::readVcf is reordering the FORMAT field of my VCF file
Scholar 5 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: From RleList to RleArray
Scholar 16 months ago, created an answer that has been accepted. For A: About methylation data processing
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Error when generate mapToGenome
Scholar 16 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Popular Question 16 months ago, created a question with more than 1,000 views. For Confusion over inconsistencies with showMethods('Rle') when loaded via GenomicRanges
Popular Question 16 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 16 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.7 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 2.7 years ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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