User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun22k
Reputation:
21,910
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Location:
Cambridge, United Kingdom
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Google Scholar Page
Last seen:
an hour ago
Joined:
4 years, 4 months 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

<prev • 2,422 results • page 2 of 243 • next >
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Comment: C: Paired analysis setup using edgeR - follow up question
... 1. I would fuse `Group` and `Visit` into a single variable and use a one-way layout. Your additive model assumes that the treatment and time are additive, but this won't be true for the most interesting genes. 2. It wouldn't hurt to run `duplicateCorrelation` again after the second `voomWithQuality ...
written 10 days ago by Aaron Lun22k
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Answer: A: Average read counts and batch-effect correction in edgeR
... Firstly, I should point out that using pseudo-counts (i.e., "classic" _edgeR_) is not the recommended way to do things anymore. Use `estimateDisp` instead of the old dispersion estimation functions, and use `glmQLFit` and `glmQLFTest` instead of `glmFit` and `glmLRT`. Now, let's correct some of you ...
written 10 days ago by Aaron Lun22k
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Answer: A: Paired analysis setup using edgeR - follow up question
... You would make life a lot easier for everyone if you formatted your experimental design more clearly, like so: ```r id <- rep(c("004", "008", "009", "022"), each=2) time <- factor(rep(c(1, 4), 4)) treatment <- rep(rep(c("Placebo", "Treatment"), each=2), 2) data.frame(id, time, treatment) ` ...
written 10 days ago by Aaron Lun22k
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Comment: C: DEseq2 for differential binding analysis ChIP seq
... I would never analyze different histone marks (or generally different protein targets) in the same linear model. What does it even mean to compare, say, H3K4me3 enrichment to H3K27me3? This is uninterpretable unless you can say that the IP efficiency is the same for both antibodies, and I very much ...
written 10 days ago by Aaron Lun22k
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Answer: A: Error in installation of scran
... You shouldn't have to install the Github versions of any packages - and in fact, this will mess up your installation, as you're mixing Bioc-devel and Bioc-release package versions. You'll probably get all sorts of warnings if you were to run `BiocManager::valid()`. Part of the problem lies in the ...
written 11 days ago by Aaron Lun22k
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Comment: C: plotPlatePosition and plate_position
... I assume that those 6 wells (H7-H12) don't even have libraries for any plate. If that is the case, `plotExplanatoryVariables` will just ignore them. It won't put zeroes, it won't do anything special - it would be as if you had a set of 90-well plates in the first place. It's not like `plotExplanator ...
written 13 days ago by Aaron Lun22k
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Answer: A: scran/scater Normalized matrix
... If you set return_log=FALSE in normalize, the "normalized counts" are available with normcounts(sce). Otherwise they're log-transformed and reported in logcounts(sce). ...
written 14 days ago by Aaron Lun22k
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Comment: C: Help analyzing RNA-seq data from FPKM values with multiple time points
... Your code is so wrong that it's difficult to describe all the errors. So, here's the correct code instead: library(limma) y <- matrix(rnorm(40000), ncol=4) # made up data. time.points <- c(0, 1, 3, 6) # numeric, NOT FACTOR. # First fit with splines. X <- splines::ns(time.points, 2) desi ...
written 14 days ago by Aaron Lun22k
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Answer: A: gene counts in Seurat after RunCCA() and AlignSubspace()
... As you well know, Seurat is not a Bioconductor package; you're better off asking the authors directly. ...
written 15 days ago by Aaron Lun22k
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Comment: C: removing rows from SingleCellExperiment container
... It seems you're trying to do: mySCE$states <- as.character(mySCE$states) # avoid factors my.new.SCE <- mySCE[,mySCE$states %in% c("S1", "S2", "S4")] my.2.cell.types <- c(S1="CellType1", S2="CellType1", S4="CellType2")[my.new.SCE$states] ...
written 15 days ago by Aaron Lun22k

Latest awards to Aaron Lun

Scholar 10 days ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 10 days ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 13 days ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Limma Voom duplicateCorrelation Design
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Scholar 7 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 7 weeks ago, created an answer that has been accepted. For A: Limma Voom duplicateCorrelation Design
Teacher 7 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 7 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 7 weeks ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Building contrasts for combined treatment groups to compare to a control
Scholar 7 weeks ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Scholar 7 weeks ago, created an answer that has been accepted. For A: Understanding and creating various comparisons with model.matrix in limma regard
Good Answer 11 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?
Scholar 11 weeks ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Scholar 11 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 11 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 11 weeks ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 11 weeks ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment

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