User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun24k
Reputation:
23,960
Status:
Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
4 years, 10 months ago
Email:
i******************************@gmail.com

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 • 2,621 results • page 1 of 263 • next >
0
votes
1
answer
33
views
1
answers
Answer: A: diffHic presplit_map.py --sig option for HiC libraries prepared with restriction
... The mapping scripts inside _diffHic_ don't support multiple restriction enzymes. Mostly because I haven't added it, but also because the split-and-map strategy is not very good when there are multiple short ligation signatures. `presplit_map.py` will identify the ligation signature (i.e., the sequen ...
written 1 day ago by Aaron Lun24k
0
votes
1
answer
77
views
1
answers
Comment: C: Limma for cell components effect on response
... Yes and yes. You may also want to log-transform the components, I would expect log-expression to increase linearly with log-abundance rather than linearly with raw abundance. ...
written 1 day ago by Aaron Lun24k
1
vote
2
answers
42
views
2
answers
Answer: A: diffHic presplit_map.py pysam.SamtoolsError
... I'm a bit bemused as well. Let's try to localize the error: - Is `HIC003_R1.fastq.bam` a valid BAM file? Try inspecting it with `samtools`. - If you opened up the Python interpreter, what happens when you do: ``` import pysam tmpdir="tmpnA4PdG" outbam=os.path.join(tmpdir, "HIC003_R1.fastq.bam") bs ...
written 4 days ago by Aaron Lun24k
0
votes
1
answer
77
views
1
answers
Answer: A: Limma for cell components effect on response
... You should throw all the cell compositions into the model at once. This protects you against co-linearity in the compositions. For example, if CD8 and CD4 T cell abundances are strongly correlated, a single model that contains terms for all cell abundances will not be able to confidently associate a ...
written 6 days ago by Aaron Lun24k
1
vote
2
answers
184
views
2
answers
Comment: C: Difference of difference, paired design
... You know, it would really help if you had provided a sample table. Let's just make one up: ``` # 6 individuals, first 3 are trained. individuals <- gl(6, 2) trained <- factor(rep(c("Y", "N"), each=6)) exercise <- factor(rep(c("before", "after"), 6)) exercise <- relevel(exercise, "before ...
written 6 days ago by Aaron Lun24k
1
vote
1
answer
84
views
1
answers
Comment: C: EdgeR - Model matrix for complex model similar to user guide 3.5 example - but m
... To follow up a bit, I would favor the much simpler formulation: ``` # Note the different 'patient' compared to James' post. phenomat2 <- data.frame( disease = factor(rep(c("healthy","disease"), c(6,9))), patient = factor(rep(c(1:5), each = 3)), treatment = factor(rep(c("Drug_A","Dr ...
written 6 days ago by Aaron Lun24k
0
votes
1
answer
103
views
1
answers
Comment: C: adjusting for confounding effects in edgeR
... > With this design, do you think additive model is enough for batch effect correction? You don't have much of a choice. The only alternative would be to combine `batch` and `group` into a single factor by `paste`ing them together, and then compare coefficients `1a` to `2a` and `1c` to `2c`. This ...
written 6 days ago by Aaron Lun24k
0
votes
1
answer
103
views
1
answers
Comment: C: adjusting for confounding effects in edgeR
... > Can I also add the batches in my additive model like this? Yes. > If yes, is it the best way to consider batch effects for a well designed study? Yes, but the design of this study has some room for improvement. The sole sample in batch B is effectively useless. > Why do you think I n ...
written 10 days ago by Aaron Lun24k
0
votes
1
answer
91
views
1
answers
Comment: C: Complex multifactorial design with random effects in Limma/voom
... > So what would be the difference of this previous approach I used with the one you suggested (apart from more easily allowing me to test all contrasts I am interested in)? More residual d.f. but stronger assumptions. > If you were to spell out the model that you suggested how would that loo ...
written 10 days ago by Aaron Lun24k
3
votes
1
answer
91
views
1
answers
Answer: A: Complex multifactorial design with random effects in Limma/voom
... Seems like your life would be easiest if you just combined the three factors of interest. ``` # Assuming you loaded the data.frame into 'df'. group <- paste0(df$Treatment, df$Region, df$Behaviour) design <- model.matrix(~0 + group + df$Hive) ``` ... and then block on `Sample_ID` in `duplicat ...
written 14 days ago by Aaron Lun24k

Latest awards to Aaron Lun

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Differential gene expression for multi-factorial experiment using edgeR
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: limma-voom duplicateCorrelation once or twice, difference?
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Correct use of tximport in combination with edgeR cpm()
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Understanding contrasts limma
Appreciated 6 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Appreciated 6 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Scholar 6 months ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma trend test with pre/post design and technical replicates
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma Model Design
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: scran: Are the log counts expression comparable among different genes within a s
Scholar 6 months ago, created an answer that has been accepted. For A: Limma design/contrast correct?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Saving output from glmTreat to a csv file?
Scholar 6 months ago, created an answer that has been accepted. For A: applying voom + limma to a block factor design in RNA-seq experiment
Teacher 6 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
Scholar 6 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Re-numbering blocking IDs on paired samples with duplicateCorrelation or design
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Limma design/contrast correct?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 132 users visited in the last hour