User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun23k
Reputation:
22,570
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Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
7 hours ago
Joined:
4 years, 6 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 • 2,484 results • page 2 of 249 • next >
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Comment: C: How to identify real cells in 10X RNA-seq ?
... > How can it be ture ? I think its impossible that cells is even more than what I put ! The most obvious explanation is that the sample contains more cells than you think. I'm not sure how you're counting your cells, but viability markers may underestimate the cell count if you have damaged cell ...
written 8 days ago by Aaron Lun23k
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Answer: A: edgeR design matrix not of full rank
... Make life easy for yourself and combine `treatment` and `time` into a single factor: ``` combo <- factor(paste0(treatment, ".", time)) design <- model.matrix(~0 + combo + patient) ``` Each of the first 9 columns represents the average log-expression of each treatment/time combination (in pat ...
written 9 days ago by Aaron Lun23k
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Answer: A: How to identify real cells in 10X RNA-seq ?
... > cellranger 2.0 think there are 3442 cells , while cellranger 3.0 think there are 10275 cells. This is a result of a change to the cell calling method in version 3, see the "Calling cell barcodes" section [here](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/late ...
written 9 days ago by Aaron Lun23k
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Answer: A: What are the methods to get count data per cell from single cell fastq given onl
... > Cell Ranger uses STAR and it seems like it does more than you would want I would say that _CellRanger_ does the necessary amount of work that needed to get a count matrix. One should not underestimate the complexity of the 10X sequencing construct, which involves at least four pieces of 10X-sp ...
written 9 days ago by Aaron Lun23k
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Comment: C: How to identify real cells in 10X RNA-seq ?
... Or you can just edit your original post, you know. ...
written 9 days ago by Aaron Lun23k
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Comment: C: How to identify real cells in 10X RNA-seq ?
... Suggest putting some paragraph breaks in your post. ...
written 9 days ago by Aaron Lun23k
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Answer: A: using limma for circular RNA analyses
... I'm not familiar with circular RNA-seq, but unless there's something radically different from standard RNA-seq, I'd say that your data set has some issues. The samples with negative log-CPMs are very different from the other replicates in the same group. This is usually a sign that something has gon ...
written 10 days ago by Aaron Lun23k
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Answer: A: Dependence of FDR and P-values on sample size
... > In case two, my results look better, when viewing the cpm values of the samples side by side, I don't understand what you mean here. > So, my question is, on reducing the data set, is it so that the FDR values also increase? In theory, no. Upon filtering, the total number of tests should ...
written 10 days ago by Aaron Lun23k
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... [This](https://doi.org/10.1093/biostatistics/kxw055) may be of interest, as well as the vignettes [here](https://github.com/MarioniLab/compareSingleCell) and [here](https://bioconductor.org/packages/devel/workflows/vignettes/simpleSingleCell/inst/doc/de.html#6_using_pseudo-bulk_counts). Note that th ...
written 11 days ago by Aaron Lun23k
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Comment: C: Paired analysis (tumor vs normal) at three different conditions with EdgeR
... Yes, the original design matrix is valid but assumes that the effects of `group` and `tissue` are additive. My design sacrifices some residual d.f. to eliminate this assumption, which is important if the tumor/normal difference is condition-specific (i.e., there is a non-zero interaction between `gr ...
written 12 days ago by Aaron Lun23k

Latest awards to Aaron Lun

Scholar 9 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 9 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 9 weeks ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Limma Voom duplicateCorrelation Design
Scholar 3 months ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Scholar 3 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 3 months ago, created an answer that has been accepted. For A: Limma Voom duplicateCorrelation Design
Teacher 3 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 3 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 3 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 3 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 3 months ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Scholar 3 months ago, created an answer that has been accepted. For A: Understanding and creating various comparisons with model.matrix in limma regard
Good Answer 4 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 4 months ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Scholar 4 months ago, created an answer that has been accepted. For A: EdgeR - blocking for multiple factors at once - Errors
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 4 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 4 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Scholar 4 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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