User: maltethodberg

gravatar for maltethodberg
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Posts by maltethodberg

<prev • 44 results • page 1 of 5 • next >
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interGeneCorrelation and voom
... I'm looking at using interGeneCorrelation to calculate correlation between sets of genes for RNA-Seq data. camera can take weights obtained via voom into account, but I was surprised to see that camera does not actually call interGeneCorrelation to do this. As the interGeneCorrelation function itsel ...
limma voom intergenecorrelation written 4 days ago by maltethodberg40
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Comment: C: limma-trend with random effects and/or array weights
... In line with the original question, which sequence of function calls would you use in that case for combining duplicateCorrelation with voom/voomWithArrayWeights? ...
written 5 weeks ago by maltethodberg40
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Comment: C: Implementing fast mathematical and statistical operations on genomic variables i
... Interesting! I am using functions operating on RleLists extensively (coverage, slice, Views, viewSums, etc), how will they be affected? ...
written 7 weeks ago by maltethodberg40
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Comment: C: Plans for multicore block processing in DelayedArray?
... Interesting! Looking forward, in order to unlock most of the features of DelayedArray (better compression + parallel block processing), it's better to use RleMatrix instead of a DataFrame of Rle's? One reason for using a DataFrame of Rle's is that it seems much faster to create than an RleMatrix. W ...
written 7 weeks ago by maltethodberg40
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Comment: C: Plans for multicore block processing in DelayedArray?
... I am only using in-memory objects at the moment, primarily DataFrame of Rle's wrapped with DelayedArray. I was actually wondering what the difference is between a DelayedArray around a DataFrame compared to an RleMatrix - conceptually they seem very similar? Is one more efficient speed or memory-wis ...
written 7 weeks ago by maltethodberg40
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Comment: C: Plans for multicore block processing in DelayedArray?
... That sounds good! I am considering rewriting an R-package I am are developing to take advantage of the new features in DelayedArray. While it is much more memory efficient than my current implementation, it is quite a bit slower. The main bottle-necks are calls to rowSums, colSums, etc on large arra ...
written 7 weeks ago by maltethodberg40
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Plans for multicore block processing in DelayedArray?
... Following up on the vignette in the devel-version for DelayedArray: Is there a timeline for implementation of multicore processing across blocks? ...
delayedarray written 8 weeks ago by maltethodberg40 • updated 7 weeks ago by Hervé Pagès ♦♦ 13k
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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 8 weeks ago by maltethodberg40 • updated 8 weeks ago by Gordon Smyth32k
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Comment: C: remove NA's from a DelayedArray
... cool thanks! ...
written 8 weeks 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 8 weeks ago by maltethodberg40

Latest awards to maltethodberg

Popular Question 5 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 19 months ago, voted at least 25 times.

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