User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun24k
Reputation:
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Location:
Cambridge, United Kingdom
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Google Scholar Page
Last seen:
7 hours ago
Joined:
4 years, 10 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 • 2,621 results • page 3 of 263 • next >
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Answer: A: Majority upregulated genes in edgeR
... The imbalance you describe isn't really an issue. 57700 genes (after filtering), 11500 DE, 8000 up-regulated? That's still less than 20% DE overall, with a ~2:1 up- to down-regulated ratio. Seems perfectly feasible to me, especially when dealing with irregular disease biology. Contrast this to ChIP- ...
written 23 days ago by Aaron Lun24k
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Comment: C: Time course experiment using limma with voom
... Yes, if you wanted to do that, block on `patient` in `duplicateCorrelation()` and put in `age` and `sex` as additive terms in the design matrix. Those things don't seem that interesting to me, though; perhaps an interaction between `wloss` and `sex` would be more fun. ...
written 25 days ago by Aaron Lun24k
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Comment: C: Combining counts from non-replicate samples in RNA-Seq analysis for a synergisti
... > Looking at my results, it appears my initial “manual” work-around combination of counts (adding SKO1/SKO2 and DKO/WT columns together) results in a similar list of genes with similar log-fold changes to setting it up in makeContrasts. I would advise against using that workaround in general; ad ...
written 25 days ago by Aaron Lun24k
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Answer: A: adjusting for confounding effects in edgeR
... An additive model is appropriate. The various factors/covariates don't seem to have strong correlations with each other, so the interpretation of the coefficients is fairly straightforward in `design`. - The intercept is the average expression in group 1. (Technically, it is the expected expression ...
written 28 days ago by Aaron Lun24k
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Answer: A: Combining counts from non-replicate samples in RNA-Seq analysis for a synergisti
... This should be a standard test for a non-zero interaction term. ``` groups <- rep(c("WT", "SKO1", "SKO2", "DKO"), each=4) design <- model.matrix(~0 + groups) colnames(design) <- sub("groups", "", colnames(design)) # just to clean up # ... Normalize, estimate dispersions, etc. ... con < ...
written 28 days ago by Aaron Lun24k
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Comment: C: differential expression between clusters (in distinct "treatments") in scRNAseq
... Well, you literally just `paste` them together. Like `paste(sce$cluster, sce$Oncogene)`. And then use the resulting vector as your grouping factor in a DE analysis, or as `cluster=` in `findMarkers()`. Then you can compare between any pair of cluster:condition combinations that you are interested in ...
written 29 days ago by Aaron Lun24k
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Comment: C: Time course experiment using limma with voom
... See my updated answer. Don't worry about the fact that the weight loss is zero at the first time point. There's no need for the model to account for this, because there's nothing there! Now, the appropriate model would be different if you wanted to account for the association of expression with the ...
written 29 days ago by Aaron Lun24k
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Answer: A: Re-numbering blocking IDs on paired samples with duplicateCorrelation or design
... **tl; dr** If you want to directly compare expression between healthy and sick patients, use `voom`. **Question 1:** I would prefer to use the `~ 0 + Patient + Group` formulation and to remove the unestimable `Healthy.Placebo` coefficient. (I'm going to assume you `relevel`ed `group` so that the si ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: Time course experiment using limma with voom
... If weight loss and time are well correlated, you're in trouble. With your experimental design, there's no way to distinguish between the effect of time - due to aging or whatever - and the effect of weight loss. The correct way to do it would be to have a control group without any diet, which would ...
written 4 weeks ago by Aaron Lun24k
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Answer: A: differential expression between clusters (in distinct "treatments") in scRNAseq
... Your post is not formatted well, so I'm going to assume you're referring to two separate contrasts: > - cluster 1 cells in "control" versus "oncogene induced" - cluster 1 cells in "control" versus cluster 2 (or any other cluster) in "oncogene induced" Just paste the cluster ID with the oncogen ...
written 4 weeks ago by Aaron Lun24k

Latest awards to Aaron Lun

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
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: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Differential gene expression for multi-factorial experiment using edgeR
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: limma-voom duplicateCorrelation once or twice, difference?
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Correct use of tximport in combination with edgeR cpm()
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Understanding contrasts limma
Appreciated 6 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Appreciated 6 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 6 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
Scholar 6 months ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma trend test with pre/post design and technical replicates
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma Model Design
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: scran: Are the log counts expression comparable among different genes within a s
Scholar 6 months ago, created an answer that has been accepted. For A: Limma design/contrast correct?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Saving output from glmTreat to a csv file?
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
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
Scholar 6 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Re-numbering blocking IDs on paired samples with duplicateCorrelation or design
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma design/contrast correct?

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