User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun13k
Reputation:
12,550
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Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
2 years, 4 months ago
Email:
a***@wehi.edu.au

I am a research associate working in computational biology at the Cancer Research UK Cambridge Institute in the United Kingdom. I am the author and maintainer of the csaw, diffHic, InteractionSet and scran 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 • 1,369 results • page 1 of 137 • next >
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Answer: A: error in Limma analysis - estimated df (df.0) for prior value of variance (s2.po
... Firstly, it's good practice to post the minimal code required to generate a problem, rather than expecting people to read other resources. Secondly, an infinite prior d.f. from limma is not an error. It is entirely possible to obtain this value if all genes have the same true variance, such that all ...
written 7 hours ago by Aaron Lun13k
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Comment: C: How to extract common genes that are DE in each comparisons?
... Please use the "add comment" button to reply to existing answers, rather than adding a new answer. de.in.all is a logical vector, so its length will obviously be the same as the number of genes. The relevant bit of information is in which elements are TRUE, i.e., which(de.in.all) if you want the in ...
written 11 hours ago by Aaron Lun13k
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Answer: A: How to extract common genes that are DE in each comparisons?
... You should be able to do something like: is.de <- decideTests(fit2, method="global") de.in.all <- rowSums(is.de!=0) == ncol(is.de) ... which will select the genes that are DE in all comparisons at a FDR of 5%. The "global" method ensures that the same significance threshold is applied to al ...
written 12 hours ago by Aaron Lun13k
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Answer: A: One replicate (one-color OR two-color) is enough to use Limma?
... In other words: If I only have replicates in one group, will limma still work? The answer is yes. limma will estimate the variance from the group with multiple replicates and use that estimate for all comparisons between groups. This will control the type I error rate assuming that the true varian ...
written 1 day ago by Aaron Lun13k
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Comment: C: searching for edgeR version 2.2.6
... I would advise updating your analysis script, rather than depending on an out-of-date version. There have been many methodological improvements that you should make use of. Probably you should do: de.tagwise <- glmLRT(glmfit.tgw, coef=4:9) ... if glmfit.tgw is the DGEGLM object produced by glm ...
written 1 day ago by Aaron Lun13k
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Answer: A: How to remmove duplicated paired end alignments
... Paired-end duplicate removal is a job that's done quite well by Picard's MarkDuplicates tool. I routinely use this for Hi-C data where the reads in each pair have been aligned separately. In your case, I would compress the SAM files, sort the alignments by position, merge the BAM files with samtools ...
written 1 day ago by Aaron Lun13k
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Comment: C: convert data frame of Entrez IDs to Gene Symbols
... In response to comment; if you want to preserve the original dimensions of myGenes, you can do something like this: coerced <- as.character(as.matrix(myGenes)) anno.result <- select(org.Hs.eg.db, keys=coerced, columns="SYMBOL", keytype="ENTREZID") new.symbols <- anno.result$SYMBOL[match(c ...
written 2 days ago by Aaron Lun13k
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Comment: C: Including novel transcripts and antisense into differential gene expression anal
... Probably best to ask a new question, but I'll give a brief answer here. These days, I perform counting with Ensembl IDs in my analyses, but there isn't a 1:1 correspondence between Ensembl and Entrez. So, I still match IDs at the start of the analysis with org.XX.eg.db, but I don't remove Ensembl-an ...
written 2 days ago by Aaron Lun13k
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Answer: A: convert data frame of Entrez IDs to Gene Symbols
... Not the prettiest sight, but a coercion to a matrix followed by a coercion to a character vector should work: anno.result <- select(org.Hs.eg.db, keys=as.character(as.matrix(myGenes)), columns="SYMBOL", keytype="ENTREZID") anno.result <- anno.result[!is.na(anno.result$ENTREZID),] You ...
written 3 days ago by Aaron Lun13k
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Comment: C: Including novel transcripts and antisense into differential gene expression anal
... Probably not. You say you want to use the normalization factors from the known genes - then, by implication, you don't trust the information provided by the antisense or novel transcripts, so it doesn't make sense to use them for normalization. Moreover, if you have a lot more novel transcripts than ...
written 3 days ago by Aaron Lun13k

Latest awards to Aaron Lun

Scholar 8 months ago, created an answer that has been accepted. For A: Adapting old Workshop to recent changes of the Limma package
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Method for batch correction
Appreciated 9 months ago, created a post with more than 5 votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: design matrix in GLM
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Method for batch correction
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Scholar 9 months ago, created an answer that has been accepted. For A: Adapting old Workshop to recent changes of the Limma package
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Scholar 9 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Scholar 9 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Scholar 10 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Scholar 10 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Scholar 10 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: edgeR - how to convert DGELRT and other classes to .csv files
Scholar 10 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Scholar 10 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Scholar 10 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?

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