User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun16k
Reputation:
16,110
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Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
3 years 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, scrancydar and beachmat packages, a contributor and co-maintainer for the edgeR and SingleCellExperiment packages, and an occasional contributor to the limma and scater packages.

Posts by Aaron Lun

<prev • 1,756 results • page 2 of 176 • next >
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Comment: C: Error when merging SCESet objects
... The next scater release will come out with the next Bioconductor release... which should be soon-ish. Next month, maybe? ...
written 7 days ago by Aaron Lun16k
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Comment: C: edgeR - MDS Plot for Count Data
... Yes, you need to filter out low-abundance genes. Otherwise the mean-variance trend looks funny. ...
written 7 days ago by Aaron Lun16k
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Comment: C: Limma for differential expression in a time-course
... Don't compare p-values between tests, that rarely makes any sense. If you want to detect genes for scenario 1, then you'll have to use an additive model (and make sure that you ignore genes with significant interaction effects). If you want scenario 2, then coef=8:12 in the interaction model is th ...
written 8 days ago by Aaron Lun16k
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Answer: A: Error when merging SCESet objects
... The combine step will identify entries of the exprs(x) and exprs(y) matrices that have the same row and column names. For these entries, the expression values need to be the same in order for the merge to succeed. Otherwise, the function doesn't know which ones to keep in the output matrix. In your ...
written 8 days ago by Aaron Lun16k
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Comment: C: goseq after edgeR
... The genome= argument is optional, it isn't needed to import a GTF file. See width. See read.table. ...
written 9 days ago by Aaron Lun16k
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Answer: A: Limma and batch effect
... I don't think your first approach is doing what you want. Extracting fit$p.value[,2] will get you the p-values corresponding to the batch effect, rather than the effect of fac. You should be using topTable with coef= to specify the coefficient to be tested (probably the last one). Now, assuming tha ...
written 9 days ago by Aaron Lun16k
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Answer: A: Limma for differential expression in a time-course
... The interaction model is not particularly helpful when testing for differences in average expression between groups. If you believe that a non-zero interaction can exist, then a difference in average expression becomes difficult to interpret; it could be driven by a shift in the "baseline" between g ...
written 10 days ago by Aaron Lun16k
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Answer: A: goseq after edgeR
... Rather than going through some web-based interface, the easiest approach to running a goseq analysis is to just install the goseq package via biocLite and follow the instructions in the user's guide. The instructions in Section 5 for non-native organisms and the case study in Section 6 should answer ...
written 10 days ago by Aaron Lun16k
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Answer: A: csaw: how does unequal sample size affect filtering filterWindows step
... When filterWindows performs independent filtering, the independence is referring to the fact that the filter does not affect the distribution of p-values when the null hypothesis is true. In other words, the type I error rate is still controlled among the true null windows/regions after filtering. T ...
written 11 days ago by Aaron Lun16k
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Comment: C: edgeR - MDS Plot for Count Data
... If you want to run estimateCommonDisp, you need to do so on the DGEList object, not the output of voomWithQualityWeights. However, there is no need to estimate the dispersion on the output of voomWithQualityWeights, use the standard limma approach instead. ...
written 14 days ago by Aaron Lun16k

Latest awards to Aaron Lun

Scholar 12 weeks ago, created an answer that has been accepted. For A: EdgeR -ANOVA-like test vs testing individual contrasts
Scholar 12 weeks ago, created an answer that has been accepted. For A: Limma Model Design
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 3 months ago, created an answer that has been accepted. For A: Limma Model Design
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: limma: same data in different formats produces different DEG-analysis results
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 3 months ago, created an answer that has been accepted. For A: Limma Model Design
Appreciated 4 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Appreciated 4 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Appreciated 4 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 4 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 4 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 5 months ago, created an answer that has been accepted. For A: limma for metabolite data
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 5 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 5 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 5 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 5 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 5 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA

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