User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun24k
Reputation:
23,720
Status:
Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
5 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 • 2,601 results • page 1 of 261 • next >
2
votes
1
answer
64
views
1
answers
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 6 hours ago by Aaron Lun24k
0
votes
1
answer
112
views
1
answers
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 2 days ago by Aaron Lun24k
1
vote
1
answer
102
views
1
answers
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 2 days ago by Aaron Lun24k
1
vote
1
answer
59
views
1
answers
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 5 days ago by Aaron Lun24k
4
votes
1
answer
102
views
1
answers
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 5 days ago by Aaron Lun24k
0
votes
1
answer
60
views
1
answers
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 6 days ago by Aaron Lun24k
0
votes
1
answer
112
views
1
answers
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 6 days ago by Aaron Lun24k
2
votes
1
answer
48
views
1
answers
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 7 days ago by Aaron Lun24k
0
votes
1
answer
112
views
1
answers
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 7 days ago by Aaron Lun24k
0
votes
1
answer
60
views
1
answers
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 7 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 280 users visited in the last hour