User: maltethodberg

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maltethodberg100
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Posts by maltethodberg

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... Thanks for the detailed comment! I don't think the the two-stage approach you suggest would be entirely appropriate here, as the two timepoints have a very different number of pairwise differences (more than twice as many difference between sites on the segment time point). Would it still be correc ...
written 1 day ago by maltethodberg100
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Correct use of Nested/Stage-wise testing with limma/stageR for 3-group design.
... I'm analysing an RNA-Seq dataset with the following study design: Three locations (e.g. A, B, C) at two different times (e.g. time 1 and 2), everything in triplicates. I'm interested in finding DE genes within each time point: A1 vs B1, A1 vs C1, B1 vs C1, and similarly for the second time point. I ...
limma decidetests stager written 6 days ago by maltethodberg100 • updated 6 days ago by Koen Van den Berge170
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Comment: C: Best way of creating a large RleMatrix
... Thank you! Does the new constructor affect how the chunks are structured? If you construct an RleMatrix from a DataFrame of Rle's, is the RleMatrix then chunked by column? ...
written 20 days ago by maltethodberg100
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Best way of creating a large RleMatrix
... What's the preferred way of creating a large RleMatrix? The documentation page ?RleMatrix only covers how make an RleMatrix from a single Rle (which doesn't work for very large RleMatrix objects) First creating a normal matrix and then coercing to RleMatrix, requires keeping the original matrix in ...
delayedarray rlematrix written 9 weeks ago by maltethodberg100 • updated 23 days ago by Hervé Pagès ♦♦ 13k
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Comment: C: bplapply with progressbar
... Picking up on this answer, is it possible to have bpapply show a progress bar similar to pbapply when using SerialCoreParam? ...
written 10 weeks ago by maltethodberg100
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Thanks for the detailed response! I'm considering updating the CAGEfightR-package from using dgCMatrix to using DelayedArray instead (giving the new addition of parallel processing and quick summaries from DelayedMatrixStats, particularly rowsum). Using RleMatrix seems like the obvious choice for re ...
written 12 weeks ago by maltethodberg100
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Comment: C: DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle
... Thank you for the detailed explanation. A few follow up question: - Why is it beneficial to store the data as a single Rle in SolidRleArraySeed? Doesn't that limit to the total size of the matrix since it spans all columns? - If you chunk a ChunkedRleArray seed by column, how is that different from ...
written 3 months ago by maltethodberg100
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DelayedArray seeds: SolidRleArraySeed vs ChunkedRleArraySeed vs DataFrame of Rle's
... After reading the vignette for DelayedMatrixStats, I'm confused about the mention of two types of RleArray seeds: SolidRleArraySeed & ChunkedRleArraySeed What's the difference between these two seeds and a simple DataFrame of Rle's as seed? Are there perfomance/memory differences between them? ...
delayedarray delayedmatrixstats written 3 months ago by maltethodberg100 • updated 3 months ago by Peter Hickey440
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Comment: C: Calling coverage on GRanges object yields small negative values
... Sorry for reviving an old thread, but I am having the same issue as described in this question. What's a good way to solve this issue if your downstream analysis depends on not having negative values? cov[cov < 0] <- 0 is pretty slow. Perhaps running round(cov) with some number of digits? ...
written 3 months ago by maltethodberg100
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Build GPos from IPos
... It would be great if one could construct a GPos from and IPos, similarly to how one can construct a GRanges from an IRanges: GRanges(seqnames=rep("chr1", 3), ranges=IRanges(start=1:3, width=1)) # Works GPos(seqnames=rep("chr1", 3), ranges=IPos(1:3)) # Doesn't work ...
genomicranges granges gpos written 3 months ago by maltethodberg100 • updated 3 months ago by Hervé Pagès ♦♦ 13k

Latest awards to maltethodberg

Popular Question 11 weeks ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Popular Question 3 months ago, created a question with more than 1,000 views. For DE for genes with very low counts using limma.
Student 5 months ago, asked a question with at least 3 up-votes. For Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
Popular Question 19 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Popular Question 19 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 2.8 years ago, voted at least 25 times.

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