User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun24k
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24,280
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Location:
Cambridge, United Kingdom
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an hour ago
Joined:
4 years, 11 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: Using edgeR or DESeq2 to analyze allele-specific expression?
... That formulation is not of full column rank. You could drop `alleleM` to get to full column rank, but the coefficients require some more work to interpret: - `individualX:timeY` represent the blocking factors as before. - `alleleP` represents the paternal/maternal log-fold change **at time 1**. Thi ...
written 3 days ago by Aaron Lun24k
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Comment: C: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... No, because you don't want to capture the variance due to the batch effect. Recall that `denoisePCA()` operates by assuming that the technical noise is random and occupies the later PCs that are ultimately discarded. A batch effect is not random and will likely occupy one of the very early (often t ...
written 4 days ago by Aaron Lun24k
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Answer: A: Is magrittr "%>%" acceptable in bioc packages?
... Ah, that's a raw nerve right there. This question is better placed in the [Bioc-devel mailing list](https://stat.ethz.ch/mailman/listinfo/bioc-devel), which is where all topics of discussion for package development should go. The support site is intended for users to ask questions about... well, u ...
written 6 days ago by Aaron Lun24k
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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 6 days 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 6 days 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 6 days 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 7 days 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 7 days 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 7 days 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 7 days ago by Aaron Lun24k

Latest awards to Aaron Lun

Scholar 15 days ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 20 days 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: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/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: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to identify real cells in 10X RNA-seq ?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Scholar 5 weeks ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 7 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 7 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Appreciated 7 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Appreciated 7 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Teacher 7 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 7 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 7 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
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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Understanding contrasts limma
Scholar 7 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Saving output from glmTreat to a csv file?
Scholar 7 months ago, created an answer that has been accepted. For A: Limma design/contrast correct?

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