User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun25k
Reputation:
24,540
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Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
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Last seen:
an hour ago
Joined:
5 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

<prev • 2,670 results • page 1 of 267 • next >
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Answer: A: Further clarification on when not to use duplicateCorrelation with technical rep
... As Gordon suggests, the diversity of possible designs makes it difficult to suggest a hard-and-fast rule. Nonetheless, here are some thoughts: **Technical replicates:** If these are generated by literally sequencing the same sample multiple times (e.g., on different lanes), just add them together a ...
written 3 hours ago by Aaron Lun25k
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
... Depends on the purpose of the DE analysis. I use `filterByExpr()` when I'm testing for differences between conditions in a replicated multi-condition scRNA-seq study, as detailed in https://osca.bioconductor.org/multi-sample-comparisons.html. This mimics a formal DE analysis of bulk RNA-seq data so ...
written 4 hours ago by Aaron Lun25k
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Answer: A: Batch Corrections (MNN) with TPM values
... For starters, you'll need to log-transform the values. The problem lies in the fact that the usual pseudo-count of 1 makes no sense for TPMs. (One could argue that it doesn't make sense in general, but it is especially nonsensical in this case, where you're adding a "count" to a non-count TPM.) I di ...
written 4 hours ago by Aaron Lun25k
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Answer: A: Bug in estimateDisp of "edgeR"? "weights' matched by multiple actual arguments
... You shouldn't be using `voom` weights in _edgeR_. That doesn't make sense. For example, the `voom` observational weights try to account for the mean-variance relationship of count data - but the NB model in _edgeR_ already captures this relationship. So using `voom` weights would over-adjust for the ...
written 9 days ago by Aaron Lun25k
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Comment: C: Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, wh
... No obvious explanation comes to mind. If I had to guess, I would say that's because the quantile normalization uses the "average" distribution across batches as the reference to correct each batch towards (when `target=NULL`). If you average across batches that do not have _exactly_ the same populat ...
written 10 days ago by Aaron Lun25k
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Answer: A: Stouffer's method weights in scran::pairwiseWilcox
... No. As in, I don't have a reference. I wouldn't be surprised if someone has done it, though, it's a pretty obvious way to weight results from multiple Wilcoxon tests. In general, all of the `scran::pairwise*` functions attempt to weight by a value that (i) depends on the number of cells in each b ...
written 10 days ago by Aaron Lun25k
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Answer: A: Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matr
... As a general rule, `block=` is always safer than `design=`. The former literally processes each block separately and combines the results, which allows us to handle differences in the mean-variance trend (in `modelGeneVar()`) or differences in variance between groups (in `findMarkers()`). The use of ...
written 17 days ago by Aaron Lun25k
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Comment: C: Different number of marker genes between same clusters
... If you are responding to an existing answer, be sure to use the "Add Comment" button, rather than adding your own answer. Anyway, as the title of the fields suggest (e.g., `stats.7$log.FDR`), these are log-p-values and log-FDRs. Obviously, if you log-transform a p-value, you would hope that the res ...
written 17 days ago by Aaron Lun25k
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Answer: A: diffHiC error in mergePairs.
... You don't give a lot of information. So I won't give much of an answer. The current release version of _diffHic_ has not changed since the release in April, so it's nothing to do with a software update. The same is true of the current release version of _rhdf5_, which is responsible for reading and ...
written 18 days ago by Aaron Lun25k
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Answer: A: Different number of marker genes between same clusters
... For starters, it would help to show code, and it would help to tag the question with the package that you're using. I'm going to guess that you're talking about `scran::findMarkers`, because the _SingleCellExperiment_ package has no such function. In `findMarkers()`, DE comparisons are performed be ...
written 18 days ago by Aaron Lun25k

Latest awards to Aaron Lun

Scholar 8 weeks ago, created an answer that has been accepted. For A: scran: excluding genes with extremely high expression during normalization?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 8 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 10 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 11 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 11 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to identify real cells in 10X RNA-seq ?
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 11 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Scholar 3 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 9 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 9 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Appreciated 9 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Scholar 9 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Appreciated 9 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Teacher 9 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 9 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 9 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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