User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun19k
Reputation:
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Location:
Cambridge, United Kingdom
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Last seen:
6 hours ago
Joined:
3 years, 7 months ago
Email:
a***@wehi.edu.au

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 • 2,064 results • page 1 of 207 • next >
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Answer: A: how to create csv file with name of gene from unique ID of lcpm ?
... Read ?write.csv. row.names: either a logical value indicating whether the row names of ‘x’ are to be written along with ‘x’, or a character vector of row names to be written. The argument needs to be a character vector. y2$genes is a data.frame, hence the error. ...
written 1 day ago by Aaron Lun19k
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Comment: C: edgeR error when trying to filter peaks with low read counts
... Use of scaleOffset() doesn't affect the cpm() call, as the latter does not use the offsets at all. The purpose of scaleOffset() is to ensure that the shrinkage of the log-fold changes is done correctly (see ?predFC). We added this function a few releases ago, so it is perhaps not surprising that oth ...
written 1 day ago by Aaron Lun19k
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Comment: C: edgeR error when trying to filter peaks with low read counts
... Don't respond to existing answers with "Add answer", use "Add comment" instead. ...
written 1 day ago by Aaron Lun19k
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Comment: C: edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
... Please respond to existing answers with "Add comment", unless you are answering your own question. If you want to do it, you'll have to do it manually, e.g., se <- SummarizedExperiment(list(counts=d$counts), colData=d$samples) Of course, this doesn't account for all the other fields that may ...
written 1 day ago by Aaron Lun19k
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Answer: A: edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
... I don't believe this is possible. The DGEList class was not designed to be a general-purpose container, and it will not recognize arbitrary user-specified fields. Perhaps there is an argument for adding direct support for SummarizedExperiment input to various edgeR functions - and indeed, this would ...
written 1 day ago by Aaron Lun19k
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Answer: A: edgeR error when trying to filter peaks with low read counts
... lib.size= should be a vector, not a matrix, see ?DGEList. With your current set-up, there is no $samples$lib.size, resulting in a library size vector of length zero. This eventually results in errors with respect to matrix dimensions. Also, you don't mention what version of edgeR you're using, but ...
written 1 day ago by Aaron Lun19k
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Comment: C: edgeR: Choice of reference group in nested model
... Looking at the first design matrix: A1: Intercept B1: Intercept + groupb A2: Intercept + groupa:sample2 B2: Intercept + groupb + groupb:sample2 So to create the null hypothesis equivalent to (A1 + A2)/2 = (B1 + B2)/2, you do: (Intercept + Intercept + groupa:sample2)/2 = (Intercept + groupb + In ...
written 2 days ago by Aaron Lun19k
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Answer: A: edgeR: Choice of reference group in nested model
... Because the second coefficient represents different things in the two design matrices. Let's look at the design matrix when 1 is the reference level for sample. Column names are: (Intercept) groupb groupa:sample2 groupb:sample2 If you examine the entries of design, you will find that the interc ...
written 2 days ago by Aaron Lun19k
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Comment: C: limma RNA-seq analysis of human data
... Just sum them up; this won't discard any information, assuming that the counts are Poisson-distributed. ...
written 2 days ago by Aaron Lun19k
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Answer: A: limma RNA-seq analysis of human data
... I don't think there's much you can do, for various reasons: Your two "replicates" for each sample are technical, not biological. At best, this means that you can only claim replication across repeated sampling of the same individuals. You cannot make general statements about the effect of the dis ...
written 3 days ago by Aaron Lun19k

Latest awards to Aaron Lun

Scholar 9 months ago, created an answer that has been accepted. For A: EdgeR -ANOVA-like test vs testing individual contrasts
Scholar 9 months ago, created an answer that has been accepted. For A: Limma Model Design
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 Model Design
Commentator 10 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 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 Model Design
Appreciated 11 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Appreciated 11 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Appreciated 11 months ago, created a post with more than 5 votes. For A: Combining newer/older RNAseq data, batch correcting
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 11 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 11 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 12 months ago, created an answer that has been accepted. For A: limma for metabolite data
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Filtering lowly expressed genes in voom-limma analysis
Scholar 12 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 12 months ago, created an answer that has been accepted. For A: limma for metabolite data
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 12 months ago, created an answer that has been accepted. For A: limma for metabolite data
Scholar 12 months ago, created an answer that has been accepted. For A: (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Limma-voom contrast confusion
Scholar 12 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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