User: maltethodberg

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Posts by maltethodberg

<prev • 51 results • page 1 of 6 • next >
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edgeR normalisation factors different between experimental groups
... I'm analysing an RNA-Seq datasets with edgeR and using calcNormFactors to estimate normalisation factors. In one of my experimental groups all samples have normalisation factors above 1,  while in another group all samples have normalisation factors below 1. Library sizes do not vary systematically ...
edger written 5 weeks ago by maltethodberg50 • updated 5 weeks ago by Aaron Lun19k
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Comment: C: Future plans for the new GPos class
... Just had look at this again: `coverage` now works on GPos-objects, but the "weight" argument behaves differently. It fails when trying to use a column as weights: pos_runs <- GRanges(c("chr1", "chr1", "chr2"), IRanges(c(1, 5, 9), c(10, 8, 15))) score(pos ...
written 6 weeks ago by maltethodberg50
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Future plans for the new GPos class
... In continuation of my previous question (https://support.bioconductor.org/p/104597/), I was wondering about the the plans for the new GPos class. I can see it has already been added to vignette, but also that it is currently being actively worked on (along with the underlying IPos object), with one ...
genomicranges gpos written 4 months ago by maltethodberg50 • updated 4 months ago by Hervé Pagès ♦♦ 13k
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coverage no longer works on GPos objects?
... After the recent update, it seems coverage no longer works on GPos objects?  library(GenomicRanges) ## Example 2: pos_runs <- GRanges("chrI", IRanges(c(1, 6, 12, 17), c(5, 10, 16, 20)), strand=c("+", "-", "-", "+")) gpos2 <- GPos(pos_runs) coverage(a ...
genomicranges gpos written 4 months ago by maltethodberg50
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Comment: C: breakTies for a Hits-object based on value in mcols?
... Thanks! So I guess that means there is no solution using breakTies - although as you write in the edited post, that seems like an obvious functionality for that function to have (The current documentation for breakTies is also a bit unclear). As was unaware of the global=TRUE argument to which.max/ ...
written 5 months ago by maltethodberg50
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Comment: C: breakTies for a Hits-object based on value in mcols?
... I get the following error when running this code: ​ > sort(hits, by = ~val, decreasing=TRUE) Error in as.vector(x) : no method for coercing this S4 class to a vector  In any case, doesn't breakTies always choose based on the index value, rather than row order? hits2 <- as(hits, "Hits") bre ...
written 5 months ago by maltethodberg50
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breakTies for a Hits-object based on value in mcols?
... Say I have Hits-object along these lines: from <- c(5, 2, 3, 3, 3, 2) to <- c(11, 15, 5, 4, 6, 11) hits <- Hits(from, to, 7, 15, sort.by.query=TRUE) For every hit, I can assign some value: mcols(hits)$val <- c(10, 11, 15, 12, 10, 10) I then want to break all ties, similar to brea ...
s4vectors hits written 5 months ago by maltethodberg50 • updated 5 months ago by Michael Lawrence10.0k
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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 6 months ago by maltethodberg50
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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 7 months ago by maltethodberg50
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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 months ago by maltethodberg50

Latest awards to maltethodberg

Popular Question 11 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 11 months ago, created a question with more than 1,000 views. For Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
Supporter 2.1 years ago, voted at least 25 times.

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