User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun20k
Reputation:
20,090
Status:
Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
3 years, 11 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 • 2,228 results • page 1 of 223 • next >
0
votes
1
answers
30
views
1
answers
Answer: A: how to run replicates at different time points
... If all of these samples are from the same study/experiment, you should run everything together. It increases the residual d.f. (i.e., the information available to estimate the residual variance), which improves power for detecting DE. ...
written 15 hours ago by Aaron Lun20k
0
votes
2
answers
31
views
2
answers
Answer: A: EdgeR Multivariate Analysis question
... First you need to decide what you mean by "Treatment B compared to Treatment A and Controls". If you want to find genes that are DE in B vs A and in B vs Controls, then you should do two separate contrasts and intersect the results (presumably also filtering on consistent sign of the log-fold change ...
written 15 hours ago by Aaron Lun20k
0
votes
1
answers
70
views
1
answers
Comment: C: Limma trend test with pre/post design and technical replicates
... Don't think in terms of fold changes. Think in terms of log-fold changes. This allows you to consider positive and negative values without any problems. Now, from the model that I described earlier, you're getting one value per patient - the log-fold change of visit 1 over baseline. You are then fi ...
written 3 days ago by Aaron Lun20k
0
votes
1
answers
70
views
1
answers
Comment: C: Limma trend test with pre/post design and technical replicates
... 1. Ah, missed that in your patients. Yes, okay. I don't deal with ordered factors much, but it seems that some care may be required in interpretation when the quadratic and cubic terms are significant. For example: X <- factor(rep(LETTERS[1:5], each=3), ordered=TRUE) Y <- rep(1:5, each=3) - ...
written 6 days ago by Aaron Lun20k
0
votes
1
answers
62
views
1
answers
Comment: C: Scater package PlotExpression
... Look. Let's assume there is a bug in the old version of scater. Even if I were to fix the bug, I would only push the bugfix to the latest version of scater. So you'd have to download and install the latest version anyway. As a developer, I can only guarantee the performance of the current versions ...
written 6 days ago by Aaron Lun20k
0
votes
1
answers
62
views
1
answers
Comment: C: Scater package PlotExpression
... Could you try using the latest version of SingleCellExperiment (1.2.*) and scater (1.8.*)? ...
written 7 days ago by Aaron Lun20k
0
votes
2
answers
89
views
2
answers
Answer: A: Limma weights, non-specific interactions
... The main problem here is that it's hard to convert a vague sense of "I don't like these proteins" into a concrete, quantitative weight. You say that you want to downweight the problematic interactors, but by how much? What does it mean to be twice as problematic? How many angels dance on the head of ...
written 10 days ago by Aaron Lun20k
0
votes
1
answers
99
views
1
answers
Comment: C: Batch Effect Correction
... Assuming that condition1 and condition2 are truly identical (i.e., both factors), all I can say is that ComBat performs some moderation on the batch effects, with the aim of stabilizing the batch effect estimates by sharing information across genes. If the moderation is strong, the observed batch ef ...
written 10 days ago by Aaron Lun20k
0
votes
1
answers
56
views
1
answers
Comment: C: time series RNA-seq allowing time offset between individuals
... See Section 9.6.2 of the limma user's guide for an example. ...
written 10 days ago by Aaron Lun20k
0
votes
1
answers
99
views
1
answers
Comment: C: Batch Effect Correction
... Well, for starters, you're using condition1 for ComBat and condition2 for removeBatchEffect. ...
written 12 days ago by Aaron Lun20k

Latest awards to Aaron Lun

Scholar 10 weeks ago, created an answer that has been accepted. For A: column nubering plotMDS
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Is Limma's removeBatchEffect() and log2() commutative?
Scholar 10 weeks ago, created an answer that has been accepted. For A: csaw::combineTests: Error: length(ids) == nrow(tab) is not TRUE
Scholar 10 weeks ago, created an answer that has been accepted. For A: edgeR normalisation factors different between experimental groups
Scholar 10 weeks ago, created an answer that has been accepted. For A: Building contrasts for combined treatment groups to compare to a control
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Is Limma's removeBatchEffect() and log2() commutative?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: edgeR normalisation factors different between experimental groups
Scholar 10 weeks ago, created an answer that has been accepted. For A: adding a description column to glmTreat output
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Scholar 10 weeks ago, created an answer that has been accepted. For A: Paired factorial design model in limma
Scholar 10 weeks ago, created an answer that has been accepted. For A: how to calculate the logFC value
Scholar 10 weeks ago, created an answer that has been accepted. For A: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to extract genes with greatest BCV?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Continuous variable interaction with Groups in design matrix
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: edgeR normalisation factors different between experimental groups
Scholar 10 weeks ago, created an answer that has been accepted. For A: Representvie gene expression value in one condition with several replicates
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Paired factorial design model in limma
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Representvie gene expression value in one condition with several replicates
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Building contrasts for combined treatment groups to compare to a control
Scholar 3 months ago, created an answer that has been accepted. For A: Building contrasts for combined treatment groups to compare to a control
Scholar 3 months ago, created an answer that has been accepted. For A: how to calculate the logFC value
Scholar 3 months ago, created an answer that has been accepted. 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: Filtering for ATAC-seq
Scholar 3 months ago, created an answer that has been accepted. For A: adding a description column to glmTreat output

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 312 users visited in the last hour