User: Peter Hickey
Peter Hickey • 380
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- Johns Hopkins University, Baltimore, USA
- Website:
- http://www.peterhickey...
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- Joined:
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Posts by Peter Hickey
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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 Hickey • 380
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... 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 Hickey • 380
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... 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 Hickey • 380
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... Thanks, Aaron. Very helpful (as always).
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written 4 days ago by
Peter Hickey • 380
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... 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 ...
written 7 days ago by
Peter Hickey • 380
• updated 7 days ago by
Aaron Lun • 21k
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... 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 Hickey • 380
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... 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 Hickey • 380
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... To clarify, was this using BiocInstaller::biocLite("DelayedArray")?
...
written 12 weeks ago by
Peter Hickey • 380
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... 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 Hickey • 380
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... 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 Hickey • 380
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