User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun19k
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Location:
Cambridge, United Kingdom
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Last seen:
3 hours ago
Joined:
3 years, 8 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 • 2,119 results • page 2 of 212 • next >
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Comment: C: Batch Correction with only one sample in a batch
... For each gene, the function estimates the correlation between samples from the same batch. I think of this as the (square root of the) percentage of the variance that is explained by the blocking factor. A larger correlation corresponds to a stronger batch effect, as you might expect. The correlatio ...
written 8 days ago by Aaron Lun19k
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Comment: C: Batch Correction with only one sample in a batch
... To add to Ryan's comments: There is probably a slight effect of retaining the samples and including a sample-specific term in the design matrix, compared to explicitly removing them. This is because the calculation of the average abundance will be different, which will probably alter (slightly) t ...
written 8 days ago by Aaron Lun19k
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Answer: A: single continuous factor
... Does design2 assumes that when the expression of protein A is 0, the gene expression level is also zero? Yes, design2 assumes that when your staining intensity for protein A, the log-average count is also zero, i.e., the expected count is 1. Where as design1 gives more correct assumption that fo ...
written 10 days ago by Aaron Lun19k
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Comment: C: markdown is coming to the support site
... Let me try writing a long line here. It's a long line, very long line, very very long line and, yes, it does wrap. Mind blown. Thanks Lucas. ...
written 11 days ago by Aaron Lun19k
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Comment: C: edgeR and DESeq2
... "In my opinion". Honestly, a Google search would have taken... all of 10 seconds. ...
written 13 days ago by Aaron Lun19k
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Answer: A: CQN and EdgeR Library Size for Normalization
... I have tended to use the total aligned reads per sample for edgeR's lib.size when performing differential binding analyses, because it is easier to interpret as sequencing depth. Any global increases or decreases in binding (or in this case, accessibility) between conditions would alter the proporti ...
written 13 days ago by Aaron Lun19k
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Comment: C: Building contrasts for combined treatment groups to compare to a control
... Yes, that's correct.   ...
written 14 days ago by Aaron Lun19k
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Yes, that is fine, calcNormFactors and cpm don't care about the groupings. ...
written 15 days ago by Aaron Lun19k
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Answer: A: how to calculate the logFC value
... You should be using the quasi-likelihood framework (estimateDisp, glmQLFit and glmQLFTest), which offers a number of advantages over the classic and LRT methods. But long story short, yes, the calculation of the log-fold change is more complicated than taking group-wise averages and comparing them. ...
written 15 days ago by Aaron Lun19k
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Answer: A: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... I don't see a problem with using cpm with log=TRUE and a large prior.count (3-5). The log-transformation provides some measure of variance stabilisation for count data, with the added bonus that differences between log-values directly represent log-fold changes (which is what we're usually intereste ...
written 15 days ago by Aaron Lun19k

Latest awards to Aaron Lun

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Finding genes respond differently to treatment between many genotype comparison
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Sparse matrices in Bioconductor objects for single-cell analyses
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using duplicateCorrelation to handle replicate samples
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: LogFC: how do you determine the cutoff for differentially expressed genes?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: design matrix in GLM
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Multi-level experiment with limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: edgeR - MDS Plot for Count Data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Design matrix and contrast for RNA knockdown experiment
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: ANOVA using edgeR
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Dealing with (blood) contamination in RNA-seq data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Can featurecounts count number of mapped reads rapidly in arbitrary regions?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Using edgeR or DESeq2 to analyze allele-specific expression?
Teacher 11 months ago, created an answer with at least 3 up-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: design matrix - control for biological replicates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Help with design matrix for two cell types, multiple treatments
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: csaw - workflow to incorporate input/control samples?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DE for genes with very low counts using limma.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Strand-aware CSAW analysis
Student 11 months ago, asked a question with at least 3 up-votes. For Duplicated author affiliations in BiocStyle-based HTML document
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Differential Pol2 pausing analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Scaling before normalisation in RNASeq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Model matrix for anova in limma
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: edgeR - how to convert DGELRT and other classes to .csv files
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Discrepancy in the output of decideTests (total not equal to sum of up/down gene
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: csaw: how does unequal sample size affect filtering filterWindows step

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