User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun15k
Reputation:
15,060
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Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
2 years, 10 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

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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... I'd bee inclined to avoid method="robust" unless you have an explicit reason to use it. Not only is it slower, the reduced efficiency of robust regression results in a decrease in the precision of the parameter estimates. This drop in precision falls outside the standard linear modelling framework ( ...
written 2 days ago by Aaron Lun15k
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Comment: C: LogFC: how do you determine the cutoff for differentially expressed genes?
... You don't need to call eBayes if you use treat. Use voom if you're working on RNA-seq data, rather than log-transforming manually. lfc is the threshold on the log-fold change (base 2), so set the value accordingly. I don't usually set method="robust" in lmFit. In general, robustification result ...
written 2 days ago by Aaron Lun15k
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Answer: A: LogFC: how do you determine the cutoff for differentially expressed genes?
... No, there is no general objective justification for any particular log-fold change threshold. Mathematically speaking, it is possible to reject the null hypothesis at any non-zero log-fold change if the variability is low enough. One could argue that small log-fold changes are not biologically relev ...
written 3 days ago by Aaron Lun15k
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Comment: C: edgeR and lack of counts ID on CPM matrix
... Reply to posts with "add comment", not "add your answer", unless you're answering your own question. You need to add the row names to the matrix (and thus the DGEList). Doing the following: y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4) rownames(y) <- paste0("X", seq_len(nrow(y))) d <- D ...
written 4 days ago by Aaron Lun15k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... Those people are misguided. Your subset approach is incorrect; for starters, there is no correction for multiple testing, but even if there was, filtering on a minimum log-fold change can inflate the actual false discovery rate. This is because the log-fold change statistic does not consider the var ...
written 4 days ago by Aaron Lun15k
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Answer: A: edgeR and lack of counts ID on CPM matrix
... If you're talking about Ensembl or Entrez IDs (or anything involving a single string), just store them as the rownames of y. These will be preserved in the output of cpm. ...
written 4 days ago by Aaron Lun15k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... For your first question, the documentation is your friend. If you read ?decideTests, it will tell you that the threshold on the adjusted p-value is 0.05. For your second question, look at the all the rows with adjusted p-values below 0.05. This will give you a set of DE genes at a FDR of 5%. In thi ...
written 4 days ago by Aaron Lun15k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... Yes, that's good. ...
written 4 days ago by Aaron Lun15k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... Read the documentation in ?treat. ...
written 5 days ago by Aaron Lun15k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... No. Don't filter in the log-fold change manually. Use treat. ...
written 5 days ago by Aaron Lun15k

Latest awards to Aaron Lun

Scholar 28 days ago, created an answer that has been accepted. For A: EdgeR -ANOVA-like test vs testing individual contrasts
Scholar 28 days ago, created an answer that has been accepted. For A: Limma Model Design
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 4 weeks ago, created an answer that has been accepted. For A: Limma Model Design
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: limma: same data in different formats produces different DEG-analysis results
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 7 weeks ago, created an answer that has been accepted. For A: Limma Model Design
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 10 weeks ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 10 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: limma for metabolite data
Teacher 10 weeks 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 for metabolite data
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 3 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 3 months ago, created an answer that has been accepted. For A: limma for metabolite data
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 for metabolite data
Scholar 3 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
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: (batch) corrections of RNA-seq data: integrating LIMMA and SVA

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