User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun19k
Reputation:
19,360
Status:
Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
13 minutes ago
Joined:
3 years, 9 months ago
Email:
a***@wehi.edu.au

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 • 2,142 results • page 1 of 215 • next >
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Comment: C: How does edgeR cpm function calculate log(CPM) values?
... Perhaps the documentation for addPriorCount may be informative regarding the prior count addition strategy. ...
written 16 hours ago by Aaron Lun19k
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Answer: A: Problem with write.fit function
... Works fine for me. library(limma) g <- gl(3, 2) y <- matrix(rnorm(length(g) * 10000), ncol=6) design <- model.matrix(~g) fit <- lmFit(y, design) fit <- eBayes(fit) results <- decideTests(fit, method = "global", adjust.method = "BH") write.fit(fit, results, "limma_results1.txt", a ...
written 2 days ago by Aaron Lun19k
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Answer: A: How to extract gene clusters (genes of similar pattern over time) once spline cu
... As currently formulated, your questions have nothing to do with testing for differential expression, so it's hard to give any recommendations on whether you are using limma correctly. I will answer what seems to be your main question, which is "how do I cluster genes with similar expression profiles ...
written 3 days ago by Aaron Lun19k
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Answer: A: EdgeR - How to set up the design matrix for a multifactorial experimental design
... Your current design matrix and contrasts seem sensible to me. The only thing I would suggest is to use the glmQLFit and glmQLFTest framework, rather than glmFit and glmLRT; see this paper for more details. ...
written 3 days ago by Aaron Lun19k
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Comment: C: How to use diffHiC with existing contact matrices?
... Please start a new question. Please show the exact command you're using, read the posting guide. ...
written 3 days ago by Aaron Lun19k
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Answer: A: edgeR for continuous independent variables
... Yes. You should be supplying the raw counts to edgeR, and these should always be positive. If there are unknown factors of variation, sva (or RUVseq, or friends) will report these for inclusion into the design matrix. You should not be using any form of corrected values as input into edgeR functi ...
written 9 days ago by Aaron Lun19k
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Comment: C: Fitted values from EdgeR
... Using cpm is the recommended way to obtain normalized expression values for other (i.e., non-DB) analyses such as clustering and dimensionality reduction. Running it as you have done with norm_counts4 is the simplest approach, so you might as well go with that. In fact, normalized.lib.sizes=TRUE is ...
written 9 days ago by Aaron Lun19k
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Comment: C: Rhtslib fails to find liblzma.dylib on Mac OSX
... Thanks Herve, looks good on my end as well. ...
written 11 days ago by Aaron Lun19k
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Answer: A: post hoc analysis on nested model
... Your pairwise comparison approach seems sensible to me. And yes, it will take a while, as you have many samples and many comparisons involving a design matrix that is not a simple one-way layout. Unfortunately, you can't get around that easily - the simplest approach would be to parallelize your com ...
written 11 days ago by Aaron Lun19k
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Comment: C: Differential ChIP-Seq Analysis with DESeq2
... It's hard to figure out what you actually did. Using a GTF file to "count the MACS results" makes no sense; I assume that what you meant was that you counted the number of reads assigned to each gene with featureCounts. I'll also assume you're referring to the UCSC annotation for your genes, I don't ...
written 11 days ago by Aaron Lun19k

Latest awards to Aaron Lun

Scholar 4 weeks ago, created an answer that has been accepted. For A: Representvie gene expression value in one condition with several replicates
Scholar 4 weeks ago, created an answer that has been accepted. For A: adding a description column to glmTreat output
Scholar 4 weeks ago, created an answer that has been accepted. For A: how to calculate the logFC value
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 4 weeks ago, created an answer that has been accepted. For A: Building contrasts for combined treatment groups to compare to a control
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Multi-level experiment with limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: design matrix in GLM
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Sparse matrices in Bioconductor objects for single-cell analyses
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Dealing with (blood) contamination in RNA-seq data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: ANOVA using edgeR
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Can featurecounts count number of mapped reads rapidly in arbitrary regions?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: design matrix - control for biological replicates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: LogFC: how do you determine the cutoff for differentially expressed genes?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Strand-aware CSAW analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Design matrix and contrast for RNA knockdown experiment
Student 11 months ago, asked a question with at least 3 up-votes. For Duplicated author affiliations in BiocStyle-based HTML document
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differential Pol2 pausing analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Scaling before normalisation in RNASeq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Model matrix for anova in limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: edgeR - how to convert DGELRT and other classes to .csv files
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: csaw - workflow to incorporate input/control samples?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Help with design matrix for two cell types, multiple treatments

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