User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun14k
Reputation:
14,330
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Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
59 minutes ago
Joined:
2 years, 8 months ago
Email:
a***@wehi.edu.au

I am a research associate working 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, scran and cydar packages, a contributor and co-maintainer for the edgeR package, and an occasional contributor to the limma and scater packages.

Posts by Aaron Lun

<prev • 1,563 results • page 1 of 157 • next >
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Answer: A: How does newSCESet calculate expression matrix
... The vignette is wrong. The exprs are log-(normalized) count values, and are closer to log2(count + 1) after adjusting the counts for differences in the library sizes between cells. They are not log-CPMs. See https://github.com/davismcc/scater/issues/110 for a related discussion. ...
written 16 hours ago by Aaron Lun14k
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Answer: A: calcAverage missing from Scater package
... No, it isn't. Make sure you're using the latest version of scater (1.4.0, running on R 3.4.0). ...
written 4 days ago by Aaron Lun14k
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Answer: A: limma for Paired Samples vs. lme
... Q1. Well, you've already done it, so I'm not sure what the problem is. Q2. This is probably due to differences in how the blocking factor is treated. In limma, the intercept represents the log-expression of the first condition in the first donor. In nlme, the random effect has a mean of zero, so th ...
written 7 days ago by Aaron Lun14k
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Answer: A: Design matrix and contrast formation in edgeR for DE analysis
... Looks fine to me. ...
written 9 days ago by Aaron Lun14k
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Comment: C: Using Combat function of SVA to remove known batch effect and using the result f
... If by "point it out", you mean "block on it", then yes. ...
written 9 days ago by Aaron Lun14k
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Answer: A: edgeR multiple coeff in "lrt <- glmLRT(fit, coef=)"
... I struggle to see the scientific merit in comparing pairs of patients. There will obviously be DE genes between patients, because everyone's different. However, these differences tell you nothing about the behaviour of the wider population, which is what we generally want to discover from experiment ...
written 9 days ago by Aaron Lun14k
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Answer: A: Using Combat function of SVA to remove known batch effect and using the result f
... If you are using edgeR, you should be supplying the original counts and blocking on the batch effect in the design matrix. Otherwise, the uncertainty of estimating the blocking coefficients will not be properly considered by the GLM fit. Blocking should not be a problem if each group contains one or ...
written 10 days ago by Aaron Lun14k
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Comment: C: Scran normalization error with computeSumFactors
... With such few samples, I don't think pooling would provide much benefit. You don't mention what type of data you've got, but if it's bulk RNA-seq data, you might as well use TMM normalization. If it's single-cell RNA-seq data... well, regardless of what statistical magic you use, there's not much yo ...
written 10 days ago by Aaron Lun14k
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Comment: C: Testing for DE genes
... Guido's plot also suggests that there is a strong pair effect. It may be worth digging into the metadata and seeing if samples were generated in batches. If you can block on the batch, you can reduce the variance estimates and improve power to detect DE genes within batches. ...
written 11 days ago by Aaron Lun14k
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Comment: C: Testing for DE genes
... In that case, there are several other possibilities: Have you filtered out low-abundance genes? Are there outlier or low-quality arrays to be removed or downweighted with arrayWeights? Is there a mean-variance trend that warrants the use of trend=TRUE in eBayes? If there are outlier variances, ...
written 11 days ago by Aaron Lun14k

Latest awards to Aaron Lun

Appreciated 2 days ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Appreciated 2 days ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Appreciated 7 days ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 12 days ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 15 days ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 4 weeks ago, created an answer that has been accepted. For A: limma for metabolite data
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 6 weeks ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 6 weeks ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 6 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 6 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Scholar 7 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 8 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Scholar 9 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Scholar 9 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 10 weeks ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA

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