User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun23k
Reputation:
23,090
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Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
4 years, 7 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 • 2,533 results • page 1 of 254 • next >
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Comment: C: Cydar normalizeBatch specifying batches
... You can see that all of your batches have the `EC` and `YC` groups, _in addition_ to the `Reference` group. All of these three groups will be used for batch normalization of the intensities, under the assumption that the intensity distribution should be the same across batches. This is why `normaliz ...
written 1 day ago by Aaron Lun23k
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... > Do you think using raw counts without summing and treating each cell as a replicate is a proper way to do it (with DESeq2 for example)? Is it "proper"? No. You're treating the cells as replicates, which is inappropriate for various reasons. The most obvious is that, if you have multiple cell t ...
written 3 days ago by Aaron Lun23k
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Comment: C: limma random effects and multi level experiments
... Set up a metadata table. Otherwise we're just guessing what your code actually does. ...
written 5 days ago by Aaron Lun23k
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Answer: A: diffHic ICE normalization PCA with NAs
... I'll level with you here. I barely remember writing this function, and what memories I do have are filled with suffering and despair. I think I wrote it because I thought the iterative correction approach might be useful for differential analyses, but it never was, and now I'm stuck with maintaining ...
written 6 days ago by Aaron Lun23k
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Answer: A: EdgeR between/within comparisons (3.5) with nested non-balanced data set
... Use `voom` and block on `patient` with `duplicateCorrelation`. This is the only way to achieve all of your desired contrasts in a single model, as you cannot compare between disease states while blocking on `patient` in the design matrix. As a bonus, this strategy will make use of the patients that ...
written 7 days ago by Aaron Lun23k
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Comment: C: Cydar normalizeBatch specifying batches
... Woah. Stop. Why are you removing the reference samples? Show me exactly what you're doing. What does your `batch.comp` look like? You should have a `"reference"` level in the factor for each batch. ...
written 7 days ago by Aaron Lun23k
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Comment: C: EdgeR between/within comparisons (3.5) with nested non-balanced data set
... And your contrast of interest is... what? ...
written 8 days ago by Aaron Lun23k
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Comment: C: Cydar normalizeBatch specifying batches
... > I therefore removed the reference samples from the batches, which could be a mistake? Yes, that is a mistake. You should have a reference sample in each batch, that's the reason for its existence. Each factor in `batch.comp` should specify which sample is the reference in that batch; see my pr ...
written 8 days ago by Aaron Lun23k
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Answer: A: Usage of doubletCells() function before or after the batch correction?
... There's a number of ways to do this, but in all cases, you should be computing doublet scores within each batch. It is obviously impossible to get a doublet consisting of cells from different batches! My favored approach is to: 1. Compute doublet scores within each batch, but do not remove them. 2. ...
written 8 days ago by Aaron Lun23k
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Answer: A: In which order should you detect empty droplets / remove barcode swapping using
... The "all barcodes" part of the documentation is just telling you to not filter on the cell barcodes, i.e., don't call cells with some other method before using `emptyDrops`. It doesn't mean you have to keep all reads for a given barcode. The correct approach is to treat the barcode swapping remova ...
written 8 days ago by Aaron Lun23k

Latest awards to Aaron Lun

Scholar 3 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 3 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 3 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Limma Voom duplicateCorrelation Design
Scholar 4 months ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Scholar 4 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 4 months ago, created an answer that has been accepted. For A: Limma Voom duplicateCorrelation Design
Teacher 4 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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 4 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Building contrasts for combined treatment groups to compare to a control
Scholar 4 months ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Scholar 4 months ago, created an answer that has been accepted. For A: Understanding and creating various comparisons with model.matrix in limma regard
Good Answer 5 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 5 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Scholar 5 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 5 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 5 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 5 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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