User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun24k
Reputation:
23,630
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Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
10 hours ago
Joined:
4 years, 9 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 • 2,594 results • page 2 of 260 • next >
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Answer: A: cross-array comparison using limma fitted values
... This is unlikely to be a meaningful comparison. At the very least, you will have technical batch effects, e.g., differences in probe design/affinity between arrays, differences in RNA extraction/RT efficiency, variation in non-specific binding from the rest of the transcriptome. So, even if you ha ...
written 9 days ago by Aaron Lun24k
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Answer: A: Is logFC a log2 fold change or some other base in scran::findMarkers
... It's the same base as the log-transformation that was used to create the `assay.type`. If you were following the standard workflow using, e.g., `scater::normalize`, then yes, this would be base 2. If you did your own thing, then it's whatever base you used to compute the input `x`. I'll mention this ...
written 13 days ago by Aaron Lun24k
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Answer: A: single cell data: adding random effects for subject with multilevel experiment d
... **Question 1:** With respect to `duplicateCorrelation`, we explored this approach (among others) [some time ago](https://academic.oup.com/biostatistics/article/18/3/451/2970368). I would say that it wasn't worth it. Running `duplicateCorrelation()` across hundreds of samples takes a long time withou ...
written 15 days ago by Aaron Lun24k
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Answer: A: Sanity Checking Mixed Factorial Proteomics Analysis Workflow Using Limma
... The _limma_ part of this only starts at `# set up model matrix for limma and ...`. Before that, there seem to be some proteomics-specific steps that I would not be qualified to answer. The data munging step is also a mystery to me as well, so I can only assume that you've done that part correctly. ...
written 18 days ago by Aaron Lun24k
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Comment: C: logCPM to CPM conversion after removeBatchEffect()
... > Instead of using a predictive model, I am more interested whether there are any significant associations. Two sides of the same coin, really. Noise in the covariate just manifests and is modeled as increased variability in the response when you're fitting a linear model. > Apparently, PRes ...
written 18 days ago by Aaron Lun24k
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Comment: C: logCPM to CPM conversion after removeBatchEffect()
... **Question 1**. There is no guarantee that the un-logged CPMs will be positive after subtracting the prior count. If you used `removeBatchEffect`, the corrected log-CPMs may well be below `log2(prior.count)`. Regarding the dispersion: I would use the tagwise dispersion, but it probably doesn't matt ...
written 19 days ago by Aaron Lun24k
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Answer: A: logCPM to CPM conversion after removeBatchEffect()
... There are two solutions. The first is to follow the instructions [here](https://support.bioconductor.org/p/81107/#81109). This will give you "batch corrected counts" for which you can compute CPMs as usual. However - do **not** be tempted to use these counts for any serious statistical analysis, for ...
written 21 days ago by Aaron Lun24k
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Comment: C: limma - blocking or regressing out nuisance variable
... No worries, the rest of the taco went down pretty quickly. Waste not, want not. Anyway, onto the thread. Some of the comments about using the Wilcoxon rank sum test are quite concerning, see Gordon's comments [here](https://support.bioconductor.org/p/121358/#121379). Even for single-cell data, the ...
written 21 days ago by Aaron Lun24k
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Comment: C: logCPM to CPM conversion after removeBatchEffect()
... Why do you want to do this? ...
written 21 days ago by Aaron Lun24k
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Answer: A: Troubles with barcodeRanks()
... I'm going to mark this as "solved by prayers to the god of filesystems". ...
written 21 days ago by Aaron Lun24k

Latest awards to Aaron Lun

Scholar 5 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 5 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 5 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma Voom duplicateCorrelation Design
Scholar 6 months ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Scholar 6 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 6 months ago, created an answer that has been accepted. For A: Limma Voom duplicateCorrelation Design
Teacher 6 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 6 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 6 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 6 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 6 months ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Scholar 6 months ago, created an answer that has been accepted. For A: Understanding and creating various comparisons with model.matrix in limma regard
Good Answer 7 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 7 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Scholar 7 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 7 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 7 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 7 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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