User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun25k
Reputation:
24,690
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Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
5 years, 3 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

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Comment: C: Question about using sorted cell bulk microarray data (ImmGen) as reference
... Y'know, **SingleR** has a `ImmGenData()` function that would save you some trouble. ...
written 3 days ago by Aaron Lun25k
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Comment: C: How does edgeR cpm function calculate log(CPM) values?
... Close, but not quite. You cannot derive the _edgeR_ log-CPMs from the naively computed CPM, because the library size is increased by twice the scaled prior count (see `?addPriorCount` for more details). ...
written 16 days ago by Aaron Lun25k
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Answer: A: error in (function (classes, fdef, mtable) unable to find an inherited method f
... Usually it's good form to format your post correctly with, y'know, new lines and stuff. Moreover, _Seurat_ is not a Bioconductor package, and none of the packages you show use _Seurat_. I am confident in saying that none of the code as shown above will generate a Seurat object at any point. I will ...
written 16 days ago by Aaron Lun25k
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Answer: A: scater cbind for singlecellexperiment objects problem
... > but it refuses to go through since mean_counts in rowData are different. Yes, and generally speaking, this is the correct behavior for a core function like `cbind`. As a programmer, I would like these core functions to be strict with their inputs to avoid ambiguities in their outputs. (IMO, th ...
written 17 days ago by Aaron Lun25k
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Comment: C: Limma residuals matrix
... > As I work with the residuals the average expression of any gene across all samples is zero. Yes, by definition, for any design matrix that can be (re)formulated with an intercept. > I al puzzled on how to calculate logFC in that case. If you only have residuals, you can't calculate the lo ...
written 17 days ago by Aaron Lun25k
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Comment: C: edgeR lable shuffling permutation test
... It's worth nothing that the CLT alone is not sufficient theoretical justification for the t-test with only "moderately large" sample size. Even if the sample means are close-to-normally distributed, there is no guarantee that the sample variance is (i) close-to-chi-squared distributed with the expec ...
written 21 days ago by Aaron Lun25k
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Comment: C: Running DropletUtils::swappedDrops() on multiplexed samples from different libra
... > this is what we do in our pipeline since it shows higher quality in results when comparing to the combined GEX and ADT analysis. Well, it's up to you, but this seems like a cell calling problem rather than a UMI counting problem. You know, you can always just run CellRanger once and re-do the ...
written 21 days ago by Aaron Lun25k
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Comment: C: interpreting FC values from glmTreat, especially unshrunk log-fold-changes
... > However I see a range of values between -10 to +10, then a jump to ~144269470 I wouldn't read too much into that. You'll notice that 144269470 * log(2) is close to 1e8, so it's probably hit one of our thresholds where we set a value to -1e8 to mimic -Inf during GLM fitting. Arbitrary but it do ...
written 29 days ago by Aaron Lun25k
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Answer: A: Running DropletUtils::swappedDrops() on multiplexed samples from different libra
... Your experimental design is fine, your analysis is strange. I don't know why you have another molecule information file for the ADTs, I would have expected CellRanger to produce a single molecule information file per sample for both gene expression and ADT molecules. This is what `swappedDrops` expe ...
written 4 weeks ago by Aaron Lun25k
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Comment: C: PCA outliers cleaning
... Reading the [book](https://osca.bioconductor.org) may give you a better background when starting scRNA-seq data analysis. ...
written 4 weeks ago by Aaron Lun25k

Latest awards to Aaron Lun

Scholar 4 months ago, created an answer that has been accepted. For A: scran: excluding genes with extremely high expression during normalization?
Scholar 4 months ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 4 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 4 months ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 4 months ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 4 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 4 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 4 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to identify real cells in 10X RNA-seq ?
Scholar 4 months ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 4 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Scholar 5 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Appreciated 11 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Scholar 11 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Appreciated 11 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: applying voom + limma to a block factor design in RNA-seq experiment

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