User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun21k
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20,740
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Location:
Cambridge, United Kingdom
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Last seen:
7 hours ago
Joined:
4 years, 1 month ago
Email:
i******************************@gmail.com

I am a research associate 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, beachmat, DropletUtils, chipseqDB and simpleSingleCell packages; a co-author and co-maintainer of the scater, SingleCellExperiment and iSEE packages; a co-maintainer of the edgeR package; a co-author of the TENxBrainData package; and an occasional contributor to the limma package.

Posts by Aaron Lun

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Answer: A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
... I'd process cells in each run separately up until the point that they need to be combined. This is actually necessary for some procedures - emptyDrops as the ambient pool will probably differ between runs; and doubletCells, as doublets can't form between runs. Processing them separately will also ma ...
written 2 days ago by Aaron Lun21k • updated 1 day ago by Steve Lianoglou12k
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Answer: A: How to calculate average log2 CPM with batch effect?
... Simply use glmFit and take the coefficients: groups <- gl(4, 2) batches <- rep(LETTERS[1:2], 4) design <- model.matrix(~0 + groups + batches) y <- matrix(rpois(8000, lambda=10), ncol=8) # making up data y <- DGEList(y) y <- calcNormFactors(y) y <- estimateDisp(y, design) fit ...
written 6 days ago by Aaron Lun21k
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Comment: C: newSCESet and SingleCellExperiment basic differences and TMM Normalization
... For your first question: get your terminology right, otherwise this discussion will be very confusing. calcNormFactors is from edgeR. It returns TMM normalization factors, one per cell. This needs to be multiplied by the library size for each cell to obtain the size factor. You can then save the siz ...
written 6 days ago by Aaron Lun21k
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Comment: C: edgeR compilation error: with g++ 4.9.2 and R-5.0 on linux platform
... Actually, edgeR compiles fine for me with gcc 4.8.5: > BiocManager::install('edgeR') Bioconductor version 3.8 (BiocManager 1.30.2), R 3.5.1 Patched (2018-09-06 r75247) Installing package(s) 'edgeR' trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/edgeR_3.23.5.tar.gz' Content ...
written 8 days ago by Aaron Lun21k
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Answer: A: newSCESet and SingleCellExperiment basic differences and TMM Normalization
... There are a number of aspects of your post that need addressing, so let's do it one at a time. The first is the switch from SCESet to SingleCellExperiment. This happened a while ago, motivated by the superiority of the SummarizedExperiment class as a general data container in terms of stability, fle ...
written 8 days ago by Aaron Lun21k
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Comment: C: nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
... 1. method is only an argument for decideTests. For topTable, the manner of the correction is unambiguous - you have a set of p-values, and you apply the Benjamini-Hochberg correction across them. 2. As mentioned in 1, method doesn't have a role here. Nonetheless, I will try to answer what seems to ...
written 17 days ago by Aaron Lun21k
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Comment: C: Batch correction when only some subjects have replicates across batches
... More or less, though for simplicity/consistency, you could might as well block on patient in duplicateCorrelation instead, which is what you would do for the actual model for the ensuing analysis. ...
written 17 days ago by Aaron Lun21k
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Comment: C: Batch correction when only some subjects have replicates across batches
... Here's a simple demonstration of the use of weighting to account for differences in variance between samples: groups <- gl(3, 4) vars <- ifelse(groups==3, 0.1, 1) # 3rd group is full of controls. ngenes <- 10000 y <- matrix(rnorm(length(groups) * ngenes, sd=sqrt(vars)), nrow=ngenes, ...
written 17 days ago by Aaron Lun21k
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Comment: C: Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
... This is covered to some extent by Section 9.5 of the limma user's guide: All the approaches considered are equivalent and yield identical bottom-line results. ... with the minor caveat that some results change slightly when you have weights, due to an approximation in contrasts.fit - see the Note ...
written 19 days ago by Aaron Lun21k
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Answer: A: Batch correction when only some subjects have replicates across batches
... This is a tricky experimental design. You're basically stuck between two extremes: The technical replicates are perfect and have negligible variance, in which case you can manually correct across batches and discard the controls before running limma on the corrected values. Technical variance do ...
written 20 days ago by Aaron Lun21k

Latest awards to Aaron Lun

Scholar 6 weeks ago, created an answer that has been accepted. For A: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
Scholar 6 weeks ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Appreciated 6 weeks ago, created a post with more than 5 votes. For European Bioconductor meeting 2017, 4 / 5 - 6 December, Cambridge, UK
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 6 weeks ago, created an answer that has been accepted. For A: Building contrasts for combined treatment groups to compare to a control
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: edgeR normalisation factors different between experimental groups
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Building contrasts for combined treatment groups to compare to a control
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: applying voom + limma to a block factor design in RNA-seq experiment
Scholar 6 weeks ago, created an answer that has been accepted. For A: how to calculate the logFC value
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Scholar 10 weeks ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: applying voom + limma to a block factor design in RNA-seq experiment
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Paired factorial design model in limma
Scholar 10 weeks ago, created an answer that has been accepted. For A: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
Scholar 10 weeks ago, created an answer that has been accepted. For A: Building contrasts for combined treatment groups to compare to a control
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups

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