User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun24k
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Cambridge, United Kingdom
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Last seen:
5 hours ago
Joined:
5 years 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: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... > In the vignette, however, multiBatchNorm is used with HVGs. Is it? Looks like it's being called with `universe`. > Wouldn't it be valid to use `denoisePCANumber` after `multiBatchPCA` with `var.tech` and `var.total` computed by taking grand means instead of means? I thought that too, see ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: scran: excluding genes with extremely high expression during normalization?
... I'll address the broad premise of your question first. A small number of genes with large counts are not a problem for normalization. In every bulk or single-cell data set, you will see the "usual suspects" show up in the most highly expressed genes, e.g., ribosomal protein genes, MALAT1, actin B, h ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: conda install of diffHic
... Seems like a conda problem to me. CRAN indicates that _blob_ 1.2.0 is available: https://cran.r-project.org/web/packages/blob/index.html ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... > In the simpleSingleCell Correcting batch effects vignette spike-ins are available. I wouldn't read too much into that. It just happened that spike-ins were available so I used them for modelling the mean-variance trend. If you don't have spike-ins, then just swap it for one of the other model ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: Feature selection across batches in simpleSingleCell "Correcting batch effects"
... Consider genes for which the null hypothesis is true, i.e., there is no biological variability such that the total variance is equal to the technical component determined by the mean-variance trend. The estimate of the variance, however, will fluctuate around the true value, meaning that this gene w ...
written 4 weeks ago by Aaron Lun24k
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Comment: C: k argument in buildSNNGraph
... Sure, but I wouldn't sweat the details. It's subject to enough extra factors that the exact interpretation can't be easily pinned down. I'd already updated the documentation to be a bit more precise but it probably doesn't really matter. ...
written 4 weeks ago by Aaron Lun24k
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Comment: C: DropletUtils' emptyDrops() fails with non-integer counts
... The Bioc-devel version (1.5.6) has been updated to round values at the very start of `emptyDrops()`. In the end, I decided that rounding everything at the start was the safest thing to do, as this would guarantee it would play nice (in practice and theory) with the remaining operations. I'm open to ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: DropletUtils' emptyDrops() fails with non-integer counts
... This is an interesting question, and it made me think about how `emptyDrops()` might integrate with _alevin_. **tl;dr** Someone, somewhere will have to coerce the data into discrete counts. The Good-Turing algorithm depends on counts. It literally counts the frequency of counts, so if the counts a ...
written 4 weeks ago by Aaron Lun24k
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Comment: C: analysis of multiple batches and multiple treatment conditions in scRNA-seq
... Is there a question here? ...
written 4 weeks ago by Aaron Lun24k
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Comment: C: RNA-seq normalization without filtering
... As Mikhael mentioned, all ratio-based normalization methods are somewhat sensitive to low counts. The most obvious problem is that ratios involving zeroes are either undefined or yield useless scaling factors of zero. Even if we were to put those aside, we now have the problem of highly discrete rat ...
written 4 weeks ago by Aaron Lun24k

Latest awards to Aaron Lun

Scholar 4 weeks ago, created an answer that has been accepted. For A: scran: excluding genes with extremely high expression during normalization?
Scholar 4 weeks ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 4 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 6 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 7 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 7 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to identify real cells in 10X RNA-seq ?
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 7 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/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
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Appreciated 8 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Scholar 8 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Appreciated 8 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Teacher 8 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 8 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 8 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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