User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun18k
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Location:
Cambridge, United Kingdom
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Last seen:
4 hours ago
Joined:
3 years, 5 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, scrancydar and beachmat packages, a co-author and co-maintainer of the scater and SingleCellExperiment packages, a contributor to and co-maintainer of the edgeR package, and an occasional contributor to the limma package.

Posts by Aaron Lun

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Comment: C: RNA-seq Batch Correction
... The quote you've taken from that paper seems to be showing what happens before correction/modelling of the batch factors. Obviously, if you simulate data for a balanced design with a batch effect, and then fail to model that batch effect, you will inflate the variance and increase conservativeness, ...
written 18 days ago by Aaron Lun18k
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Comment: C: Beachmat install / compile issue
... My guess is that the loader is still using the old libstdc++ (the 6 on the end has nothing to do with GCC 6, see https://gcc.gnu.org/onlinedocs/libstdc++/manual/abi.html). I can't say that I've run into this before; Dr Google suggests modifying LD_LIBRARY_PATH, but it seems you've already done that. ...
written 18 days ago by Aaron Lun18k
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Comment: C: Removing batch effects from microarray data based on only a subset of samples
... A simple explanation is that the batch effect differs between different lines. This is not particularly surprising for patient-derived lines, which may be quite heterogeneous in their response to differences in culture conditions, etc. If we assume that CON LINE X is related to EXP LINE X, you can a ...
written 18 days ago by Aaron Lun18k
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Answer: A: RNA-seq Batch Correction
... I won't spreak for other analyses you might want to do with RNA-seq data; but for differential expression analyses, you should not use batch-corrected data. This is because the batch correction does not account for the uncertainty of the estimation of the batch effect, which usually results in antic ...
written 18 days ago by Aaron Lun18k
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Comment: C: Allele Specific Expression Using edgeR
... I don't quite understand how your question differs from the setup in the original post. When you're talking about groups, are you referring to your genotypes? If so, and you want to determine whether genotype has an effect on ASE, then you should just use the approach I've described above. After all ...
written 18 days ago by Aaron Lun18k
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Comment: C: two factor chip with diffbind and edgeR (or DESeq2).
... There seem to be a series of misunderstandings here, so let me clarify. Yes, edgeR does expect count data. But you can still compare log-fold changes between conditions if you set up your GLM correctly. It's equivalent to looking for a significant interaction term if one of your factors is the Ch ...
written 19 days ago by Aaron Lun18k
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Answer: A: two factor chip with diffbind and edgeR (or DESeq2).
... What do you mean by each individual ChIP-seq run? The ChIP sample and its negative control? If so, the answer is technically yes. You can use the "run" as the blocking factor and have another set of terms for the treatment-specific log-fold change of the ChIP over the control. This can be fed throug ...
written 19 days ago by Aaron Lun18k
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Comment: C: edgeR design matrix and contrasts: how to make contrast between groups that aren
... For your first question; yes, a model without an intercept is perfectly fine. You just have to adjust your interpretation of the coefficients, as each Treatment* coefficient should now represent the average expression of the corresponding group. Contrasts between groups should then be easy to set up ...
written 19 days ago by Aaron Lun18k
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Comment: C: Beachmat install / compile issue
... Please respond to existing answers with "add comment", unless you're answering your own question. The second failure message is much more familiar, see https://support.bioconductor.org/p/104005/ for a solution. In brief, your newly built beachmat library is trying to link to Rhdf5lib built using yo ...
written 19 days ago by Aaron Lun18k
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Comment: C: Best way to design a contrast matrix for analysis of dataset
... Please respond to existing answers using the "Add comment" button, unless you're answering your own question. Anyway: the results you've shown don't make much sense to me. I don't understand how you managed to get a "variable lengths differ" error when you only have one variable (groups) in your ...
written 20 days ago by Aaron Lun18k

Latest awards to Aaron Lun

Scholar 7 months ago, created an answer that has been accepted. For A: EdgeR -ANOVA-like test vs testing individual contrasts
Scholar 7 months ago, created an answer that has been accepted. For A: Limma Model Design
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 8 months ago, created an answer that has been accepted. For A: Limma Model Design
Commentator 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 8 months ago, created an answer that has been accepted. For A: Limma Model Design
Appreciated 9 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Appreciated 9 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Appreciated 9 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 9 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 9 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 10 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 10 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 10 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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