User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun17k
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Cambridge, United Kingdom
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Last seen:
7 hours ago
Joined:
3 years, 2 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 contributor and co-maintainer for the edgeR and SingleCellExperiment packages, and an occasional contributor to the limma and scater packages.

Posts by Aaron Lun

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Comment: C: Two-way anova 2x2 design with limma
... This diverges from the topic of the original post, so I would suggest posting a new question. ...
written 3 days ago by Aaron Lun17k
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Comment: C: Two-way anova 2x2 design with limma
... Use "Add comment" to respond to existing answers. Don't "Add your answer" unless you're answering your own question. F-statistics and p-values can be obtained with appropriate settings of coef in topTable. For example, coef=2 will be equivalent to Strain, coef=3 will be equivalent to Treatment, a ...
written 4 days ago by Aaron Lun17k
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Answer: A: How to use limma to do regularization for Ballgown
... First, do "regularization" and "normalization" has the same meaning? No. Normalization refers to the removal of uninteresting technical biases prior to further analyses. For differential analyses, this usually refers to removal of biases between samples (e.g., differences in sequencing depth, compo ...
written 4 days ago by Aaron Lun17k
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Answer: A: Raw count data for SC3 and SingleCellExperiment set problem
... For the SingleCellExperiment side: the error message is telling you that it can't find the relevant assay. This means that your SingleCellExperiment doesn't have a matrix named normcounts in the assays slot, hence normcounts(sce) fails. Admittedly the error message could be more informative, though ...
written 8 days ago by Aaron Lun17k
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Comment: C: Interpretation of the log fold change for a time course/factorial design analysi
... Regarding your contrast matrix: yes, this looks fine, provided that you are willing and able to interpret differences of differences of differences (i.e., log-fold changes). I would suggest reporting all the individual log-fold changes as well, e.g., for Dif_F_M_3B, you should also show, in the resu ...
written 8 days ago by Aaron Lun17k
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Answer: A: Interpretation of the log fold change for a time course/factorial design analysi
... Obviously, they will be different. Your inter-sex comparison is: (Stimulated.3.F-Stimulated.0.F)-(Stimulated.3.M-Stimulated.0.M) ... while your individual log-fold changes are calculated as: (Stimulated.3.F-Stimulated.0.F)-(Control.3.F-Control.0.F) # Female (Stimulated.3.M-Stimulated.0.M)-(Cont ...
written 8 days ago by Aaron Lun17k
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Answer: A: Two-way anova 2x2 design with limma
... There is no Section 8.7 in the user's guide. The example code seems to come from 9.5.2. If you want a two-way ANOVA, you will want to drop all non-intercept terms, so that the null is that all factor combinations have the same mean expression. This can be done by setting coef=2:4 in topTable with ei ...
written 8 days ago by Aaron Lun17k
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Answer: A: Strange distribution of logFC
... You have a very strange way of constructing your CSV file; I will just assume that HPcounts actually contains the gene-wise read counts, and not some strange coercion of gene names into integers. If this is the case, then your log-fold change histogram simply indicates that you have lots of DE gene ...
written 8 days ago by Aaron Lun17k
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Answer: A: RNASeq interaction between factors with edgeR when cpms tend to zero
... You will run into this problem whenever you have a fitted value of zero (i.e., all counts are zero for that group). This is because the interaction terms are equivalent to differences (between genotypes) in the log-fold changes (between time points). As soon as zeroes get involved, the definition of ...
written 9 days ago by Aaron Lun17k
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Comment: C: Strange distribution of logFC
... Well, it can't be right, because you have: design<-model.matrix(~0+group) PvsH<-makeContrasts(P-H, levels = design) colnames(design)<-levels(group) ... which doesn't make sense, because the column names from model.matrix should be groupP and groupH before you rename them. So the call to ...
written 9 days ago by Aaron Lun17k

Latest awards to Aaron Lun

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