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User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun22k
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22,170
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Location:
Cambridge, United Kingdom
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Last seen:
4 minutes ago
Joined:
4 years, 5 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 • 2,447 results • page 1 of 245 • next >
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Comment: C: Usability of ERCC spike-ins in standard RNAseq experiments
... If you're cheap, you could just measure the RNA concentration with a Nanodrop (or Bioanalyzer, or whatever your tool of choice is). Divide the concentration by the number of cells in your sample to get the RNA content per cell. This allows you to quantify changes in RNA content between conditions - ...
written 1 day ago by Aaron Lun22k
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Answer: A: Adding labels on clusters in a t-SNE plot and changing colors
... Text labels can be added via `geom_text` or `annotate`, provided you know the coordinates you are interested in. For example, the next version of `scater::plotReducedDim` provides a `text_by=` argument that adds an identifying label at the centre of each cluster, which is useful in cases where there ...
written 1 day ago by Aaron Lun22k
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Answer: A: scater error: invalid rownames length
... It works for me. You haven't posted your `sessionInfo()`, but I'd suggest you: - Check that you are `BiocManager::valid()`, and fix any problems otherwise; or - Forcibly reinstall the relevant packages, as suggested [here](https://support.bioconductor.org/p/101813/#102033). ...
written 1 day ago by Aaron Lun22k
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Answer: A: What is the "linear model" part used for in Limma?
... This is a site for software questions rather than statistical education. If you want to learn about linear models, there are resources available elsewhere - a quick Google of "linear models" gives a number of helpful links. Here's [one](https://github.com/cambiotraining/stats-intro/blob/master/Day3/ ...
written 2 days ago by Aaron Lun22k
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Answer: A: HDF5Array Single cell experiment objects - can on-disk files change?
... Any non-delayed operations will be realized to the specified backend. By default, this is an ordinary matrix, represented fully in random access memory. If you do: ``` setRealizationBackend("HDF5Array") ``` ... you will dump results into a `HDF5Matrix`. Results will be dumped into a file specified ...
written 7 days ago by Aaron Lun22k
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Answer: A: edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
... Methods like TMM normalization (in `calcNormFactors()`) or median-based normalization (in _DESeq_) were designed for exactly the scenario you describe. If one sample has more hemoglobin mRNAs, the coverage of all other genes will be suppressed when the total amount of sequencing resource is fixed. T ...
written 7 days ago by Aaron Lun22k
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Comment: C: Silhouette Plots for Clustering Quality (Multiple Algorithm)
... I think you have your ideas mixed up here. To clarify: `buildSNNGraph` uses the Euclidean distance to identify pairs of cells with shared neighbours. It creates a link between these paired cells, weighted based on the maximum average rank of the set of shared neighbours. (That is, a pair of cells t ...
written 8 days ago by Aaron Lun22k
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Answer: A: Best practices for sharing RMarkdown-based supplemental PDFs?
... I can't resist the temptation to point out Bioconductor's workflow packages: https://www.bioconductor.org/packages/release/BiocViews.html#___Workflow These are continuously compiled with the latest versions of all the packages, thus ensuring that the code can always be executed on an independent s ...
written 14 days ago by Aaron Lun22k
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Answer: A: Highly uneven mapping rates and counts between samples
... I'll answer from the _limma_ side. There's a variety of possibilities: - Using `voomWithQualityWeights()` will help if the reduction in sample quality manifests as increased variation without introducing bias. This will downweight the contribution of the affected samples to the variance estimate. - ...
written 16 days ago by Aaron Lun22k
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Comment: C: Paired analysis setup using edgeR - follow up question
... Yes, double use of `voom` and `duplicateCorrelation` is fine. ...
written 16 days ago by Aaron Lun22k

Latest awards to Aaron Lun

Scholar 6 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 6 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 6 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Limma Voom duplicateCorrelation Design
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Scholar 11 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 11 weeks ago, created an answer that has been accepted. For A: Limma Voom duplicateCorrelation Design
Teacher 11 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 11 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 11 weeks ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
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
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
Scholar 11 weeks ago, created an answer that has been accepted. For A: Understanding and creating various comparisons with model.matrix in limma regard
Good Answer 3 months 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 3 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Scholar 3 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Building contrasts for combined treatment groups to compare to a control
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 3 months 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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