User: Aaron Lun
Aaron Lun • 21k
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- Cambridge, United Kingdom
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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, scran, cydar, 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
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... You would do well to understand the code before you try to use it. The scenario in 9.6.2 is not the same as your experimental design, it is not a copy-and-paste situation. Clue: X and Group are redundant.
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written 1 day ago by
Aaron Lun • 21k
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... Your diagnosis is correct, the rle function does some weird things with the names. The next version (i.e., in BioC 3.9) of the package will remove the names from each vector in favour of returning a DataFrame where the row names are the column names of the input matrix. (The knee and inflection poin ...
written 1 day ago by
Aaron Lun • 21k
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... Those don't seem to be Biocondcutor packages, so you'd have to ask the authors directly.
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written 2 days ago by
Aaron Lun • 21k
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Answer:
A: EstimateDisp and glm
... Try reading:
?estimateDisp
The dispersion estimation section of the workflow.
Section 2.10.2 of the edgeR user's guide.
The relevant paper.
If you still don't get it, you should probably discuss your difficulties with your professor (it's their job, after all) before asking random strangers ...
written 3 days ago by
Aaron Lun • 21k
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... 1) No (don't subset to $E, repeat voom and duplicateCorrelation), and no.
2) No, scaling normalization is not additive. It is not valid to apply one set of normalization factors on top of another.
3) No, it doesn't make much sense to compare log-fold changes of genes to spike-ins.
You should th ...
written 3 days ago by
Aaron Lun • 21k
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... AFAIK, all of the packages you listed in your question are designed for analyzing interaction intensities - which is, after all, the purpose of doing Hi-C in the first place. I don't think they have any functions to perform/refine a genome assembly from Hi-C data. In fact, I don't know of many Bioco ...
written 5 days ago by
Aaron Lun • 21k
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... Where did the FASTA files come from? Once you've done the alignment, the sequence of the assembly has nothing to do with Hi-C data analysis. If you want to get subsequences, use the relevant functions from Biostrings.
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written 5 days ago by
Aaron Lun • 21k
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... If you're talking about computeSumFactors; that function lives in scran, not scater. In addition, you should be supplying the raw counts (not scaled, not transformed) to this function, see the various examples at https://bioconductor.org/packages/simpleSingleCell.
So if you're starting from the raw ...
written 5 days ago by
Aaron Lun • 21k
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... Each row and column is a bin. You can call anchors to get the genomic coordinates.
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written 5 days ago by
Aaron Lun • 21k
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... You don't have replicates, so you can't use the design from 9.6.1. Assuming control is zero-time, the best you can do is to fit a spline with 2 degrees of freedom (see 9.6.2). From then on, it's a case of running eBayes and dropping the spline coefficients in topTable. Personally I would just assume ...
written 6 days ago by
Aaron Lun • 21k
Latest awards to Aaron Lun
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7 weeks ago,
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For A: edgeR normalisation factors different between experimental groups
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7 weeks ago,
created an answer with at least 3 up-votes.
For A: Building contrasts for combined treatment groups to compare to a control
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For A: applying voom + limma to a block factor design in RNA-seq experiment
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For A: Is Limma's removeBatchEffect() and log2() commutative?
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For A: Representvie gene expression value in one condition with several replicates
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For A: How to extract genes with greatest BCV?
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For A: Understanding and creating various comparisons with model.matrix in limma regard
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For A: EdgeR - blocking for multiple factors at once - Errors
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For A: applying voom + limma to a block factor design in RNA-seq experiment
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7 weeks ago,
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For A: EdgeR - blocking for multiple factors at once - Errors
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For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
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For A: limma barcodeplot(): calculation of enrichment score
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11 weeks ago,
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For A: How to extract genes with greatest BCV?
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11 weeks ago,
created a post with more than 5 votes.
For A: edgeR normalisation factors different between experimental groups
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11 weeks ago,
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For A: applying voom + limma to a block factor design in RNA-seq experiment
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3 months ago,
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For A: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
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3 months ago,
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For A: how to calculate the logFC value
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3 months ago,
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For A: Building contrasts for combined treatment groups to compare to a control
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3 months ago,
created an answer with at least 3 up-votes.
For A: applying voom + limma to a block factor design in RNA-seq experiment
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Representvie gene expression value in one condition with several replicates
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Building contrasts for combined treatment groups to compare to a control
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