User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun21k
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Cambridge, United Kingdom
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10 hours ago
Joined:
4 years, 2 months ago
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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 • 2,325 results • page 2 of 233 • next >
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Comment: C: csaw spike-in normalization
... The size factors are fine and can be transferred, as it directly represents the common scaling bias for the two genomes. The same logic underlies the transfer of normalization factors when the library sizes are the same. If the scaling bias is different between genomes, you shouldn't be using spike- ...
written 14 days ago by Aaron Lun21k
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Answer: A: csaw spike-in normalization
... Just set the library sizes for the foreign genome to the library sizes for your reference genome, before computing the normalization factors. This is allowable because the library sizes themselves are not really important - rather, the important thing is the product of the library sizes and normaliz ...
written 15 days ago by Aaron Lun21k
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Answer: A: edgeR package fails to load after install
... This is a very unusual error that I have not seen before. I would say that there is a problem with your GCC set-up - maybe because it's not linking to the correct C++ standard library? - so you'll have to talk to your sysadmin or whoever set up your build system. ...
written 15 days ago by Aaron Lun21k
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Comment: C: Predict circadian expression with edgeR
... There's no need to use the log-fold changes for what you want to do. You have the coefficients of the fitted GLM, so you can just compute a linear combination of terms for the given genotype. Specifically: exprs_WT_time = Control + Control:ZT_cos * X + Control:ZT_sin * Y where Control, Control:ZT ...
written 15 days ago by Aaron Lun21k
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Comment: C: Multi-factor with interaction model in EdgeR and DESeq2
... I'll chip in here - yes, edgeR was able to do this in 2015. The capability was there when I started working on edgeR in earnest (2013, maybe?), at which time I migrated all of the existing R code to use C++. As for the specific analysis; I also suspect that you have not been performing your analysi ...
written 16 days ago by Aaron Lun21k
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Answer: A: Predict circadian expression with edgeR
... I assume that you're talking about differential expression between WT and KO, and that the (co)sine functions are as usual for some constant frequency. The interpretation is pretty simple; your log-fold changes are the differences between the two genotypes if there were no time effect. This must be ...
written 16 days ago by Aaron Lun21k
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... This is a standard case of linear dependencies between coefficients. You can see how the intercept is equal to the sum of Pair_Name223 and SourceTissue. This means that there are infinitely possible solutions to the linear system that minimize the sum of squares. For a given intercept value, you cou ...
written 16 days ago by Aaron Lun21k
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Comment: C: Differentiating between batch and treatment effects in edgeR, DESeq2
... Just to be absolutely clear - I say "re-sequence", but I really mean "do everything at the same time for a given batch". Do not do something like "resequence A's existing libraries but for C perform library preparation and sequencing". This will result in hierarchical batch effects that are even mor ...
written 16 days ago by Aaron Lun21k
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... aov does type I sequential ANOVA, where it tests factors in order (i.e., Condition alone, then Condition + Source, and so on). So the reported statistics for Condition don't even consider the effect of the other factors, which was your entire problem in the first place. You can see this pretty clear ...
written 19 days ago by Aaron Lun21k
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Comment: C: Limma Design Matrix for Paired Samples with Confouding Factors
... Your second analysis (without blocking on pair) is probably very anticonservative. If the pair effect is strong, samples from the same pair are going to be highly correlated. If the design matrix does not know about the pairing, the model will not consider these correlations and will effectively ove ...
written 20 days ago by Aaron Lun21k

Latest awards to Aaron Lun

Scholar 6 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Scholar 6 weeks ago, created an answer that has been accepted. For A: limma barcodeplot(): calculation of enrichment score
Scholar 6 weeks ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: edgeR normalisation factors different between experimental groups
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 10 weeks ago, created an answer that has been accepted. For A: Building contrasts for combined treatment groups to compare to a control
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 10 weeks ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Building contrasts for combined treatment groups to compare to a control
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: applying voom + limma to a block factor design in RNA-seq experiment
Scholar 10 weeks ago, created an answer that has been accepted. For A: how to calculate the logFC value
Scholar 10 weeks ago, created an answer that has been accepted. For A: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: edgeR normalisation factors different between experimental groups
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Appreciated 10 weeks ago, created a post with more than 5 votes. For European Bioconductor meeting 2017, 4 / 5 - 6 December, Cambridge, UK
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Good Answer 3 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 3 months ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Scholar 3 months ago, created an answer that has been accepted. 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: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
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

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