User: maltethodberg

gravatar for maltethodberg
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UCPH
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3 hours ago
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1 year, 7 months ago
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Posts by maltethodberg

<prev • 37 results • page 1 of 4 • next >
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limma-trend with random effects and/or array weights
... I am doing differential expression on a fairly large RNA-Seq dataset, where multiple organs are obtained from the same mice. I would like to model the effects of individual mice using limma's random effects via duplicateCorrelation. As library sizes are very consistent across all samples (and I migh ...
limma duplicatecorrelation arrayweights limma-trend written 2 days ago by maltethodberg40 • updated 1 day ago by Gordon Smyth31k
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Comment: C: remove NA's from a DelayedArray
... cool thanks! ...
written 4 days ago by maltethodberg40
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Comment: C: Passing multiple arguments (like mapply) to the MAP-function in GenomicFiles.
... I found a somewhat hacky workaround: If you have a named file list (i.e. named BigWigFileList) you can pass the the names to the files argument and use that as an index to retrieve correct values from additional lists or vectors in ... Passing the index directly fails, since files must be a characte ...
written 5 days ago by maltethodberg40
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remove NA's from a DelayedArray
... Given that subsetting works slightly different for a DelayedArray compared to a matrix, is there a good alternative to m[is.na(m)] <- 0 for replacing NA's in  a DelayedArray? ...
delayedarray written 6 days ago by maltethodberg40 • updated 6 days ago by Hervé Pagès ♦♦ 12k
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rowsum or similar for RleArray?
... I'm experimenting with the new RleArrays from DelayedArray, and I was happy to see most operations work seamlessly just like a normal matrix.  I often use the the very fast rowsum function to aggregate rows of matrix, but this does not seem to work on an RleArray. Is there an alternative to the row ...
delayedarray rowsum written 22 days ago by maltethodberg40 • updated 20 days ago by Hervé Pagès ♦♦ 12k
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Passing multiple arguments (like mapply) to the MAP-function in GenomicFiles.
... reduceByRange with iterate=TRUE is a great way to analyse a collection of large files on laptop.     Say I have a set of files and a set of ranges. In addition, for every file I have an additional variable, say a normalisation factor, that can't be calculated on each individual range/file combina ...
genomicfiles reducebyrange written 25 days ago by maltethodberg40 • updated 24 days ago by Valerie Obenchain ♦♦ 6.2k
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Comment: C: Getting errors with makeTxDbFromBiomart
... Was this ever fixed? ...
written 7 weeks ago by maltethodberg40
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Parallel version of viewApply?
... I'm using viewApply to apply a function on each element of a SimpleRleViewsList. The function is rather slow, so I was wondering whether there was a way to execute viewApply in parallel (or something similar)?   ...
biocparallel viewapply written 4 months ago by maltethodberg40
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Gviz: Plot features with thin and thick lines
... I have a BED-like GRanges that looks like this:   GRanges object with 4957 ranges and 1 metadata column: seqnames ranges strand | thick <Rle> <IRanges> <Rle> | <IRanges> SPAC212.12.1 I [15 ...
gviz written 6 months ago by maltethodberg40
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sva: Parallel execution of sva()-function fails.
... I have been trying to calculate SVs using the sva-package in parallel, but no matter what backend I use, it always fails. Consider for examples this example code based on the vignette: library(parallel) library(BiocParallel) library(sva) library(bladderbatch) data(bladderdata) # Data from the vig ...
sva parallel written 7 months ago by maltethodberg40 • updated 7 months ago by Martin Morgan ♦♦ 20k

Latest awards to maltethodberg

Popular Question 3 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 17 months ago, voted at least 25 times.

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