User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun18k
Reputation:
17,810
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Location:
Cambridge, United Kingdom
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Last seen:
10 hours ago
Joined:
3 years, 5 months ago
Email:
a***@wehi.edu.au

I am a research associate working in the field of computational biology at the Cancer Research UK Cambridge Institute in the United Kingdom. I am the author and maintainer of the csaw, diffHic, InteractionSet, scrancydar and beachmat packages, a co-author and co-maintainer of the scater and SingleCellExperiment packages, a contributor to and co-maintainer of the edgeR package, and an occasional contributor to the limma package.

Posts by Aaron Lun

<prev • 1,976 results • page 1 of 198 • next >
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Answer: A: SingleCellExperiment object cannot be used by Scater package?
... I'm not sure I understand how you managed to get this error message. Are you using the latest version of scater (1.6.3)? The only error message in the current release version of the calculateQCMetrics function is "object must be a SingleCellExperiment". I assume you are using an older version of the ...
written 2 days ago by Aaron Lun18k
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Answer: A: Downstream analysis after using mnnCorrect()
... Before we start: the input should be scale-normalized prior to supplying them to mnnCorrect (e.g., using library sizes or, even better, size factors). Maybe the documentation for mnnCorrect could have been more clear in this respect - but if you're using the scater/scran framework, you should have a ...
written 3 days ago by Aaron Lun18k
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pkgDepTools does not consider LinkingTo: fields
... Pretty much as the title says; it would be nice to see an option in pkgDepTools to capture relationships in the LinkingTo field. For example: library(pkgDepTools) library(BiocInstaller) biocUrl <- biocinstallRepos()["BioCsoft"] biocDeps <- makeDepGraph(biocUrl, type="source", dosize=FALSE) stu ...
pkgdeptools linkingto written 7 days ago by Aaron Lun18k • updated 7 days ago by Martin Morgan ♦♦ 21k
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Comment: C: edgeR - comparing treatment groups across multiple populations
... You need to divide allpops_contrast by 3 to get the average treatment log-fold change across populations. ...
written 12 days ago by Aaron Lun18k
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Answer: A: edgeR - comparing treatment groups across multiple populations
... Your two approaches are making different assumptions. In particular, your blocking model assumes that the effect of treatment is the same in each population; this is not the case when you perform separate analyses of each population. It sounds as if the treatment effect does differ between populati ...
written 12 days ago by Aaron Lun18k
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Answer: A: edgeR - problems with coefficients and decideTests
... There are a number of errors with your code: You are using an ancient version of edgeR, we are on version 3.20.8 now. Updating your installation will solve the problem with decideTests, which has been updated to work with GLMLRT objects. glmFit doesn't take a coef= argument, as far as I remember ...
written 12 days ago by Aaron Lun18k
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Answer: A: read.delim taking infinite time in edgeR analysis
... read.delim is a function from the utils package, rather than edgeR, so this is not really an edgeR problem. You'd be better off asking this question in a more general R programming forum, e.g., StackOverflow. I am not aware of any circumstances that cause read.delim to hang; I would suggest checkin ...
written 12 days ago by Aaron Lun18k
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Comment: C: Best way to design a contrast matrix for analysis of dataset
... You should be doing ~ 0 + groups. ...
written 15 days ago by Aaron Lun18k
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Comment: C: Beachmat install / compile issue
... I wonder what happens when you look at the beachmat shared library. Try cloning from https://github.com/LTLA/beachmat (use the RELEASE_3_6 branch); run R CMD INSTALL beachmat/; enter src and see what ldd beachmat.so gives you. I get the following stuff: linux-vdso.so.1 => (0x00007fffb1dfd000) ...
written 16 days ago by Aaron Lun18k
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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... Yes, or using GreyListChIP if you are particularly concerned about changes in chromatin state. The idea is to simply remove problematic regions with high input coverage, rather than trying to be too clever about it and force the inputs into the differential analysis somehow. ...
written 16 days ago by Aaron Lun18k

Latest awards to Aaron Lun

Scholar 7 months ago, created an answer that has been accepted. For A: EdgeR -ANOVA-like test vs testing individual contrasts
Scholar 7 months ago, created an answer that has been accepted. For A: Limma Model Design
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 8 months ago, created an answer that has been accepted. For A: Limma Model Design
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: limma: same data in different formats produces different DEG-analysis results
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 8 months ago, created an answer that has been accepted. For A: Limma Model Design
Appreciated 8 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Appreciated 9 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Appreciated 9 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 9 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 9 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 9 months ago, created an answer that has been accepted. For A: limma for metabolite data
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 10 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 10 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA

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