User: Rory Stark

gravatar for Rory Stark
Rory Stark790
Reputation:
790
Status:
Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Last seen:
3 days, 1 hour ago
Joined:
6 years, 6 months ago
Email:
r*********@cruk.cam.ac.uk

Posts by Rory Stark

<prev • 54 results • page 1 of 6 • next >
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Answer: A: Consensus Peakset DIffBind
... With `minOverlap=.3`, you will keep peaks called in at least 3 Control samples (peaks only called in 1 or 2 Control samples will not be included), and at least 2 of the Treated samples (peaks only called in 1 Treated sample will not be included). If you only ewant to exclude peaks called in a single ...
written 21 days ago by Rory Stark790
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Answer: A: Loading sample sheet in DiffBind
... This a a 5-year old R environment, and no longer supported. If you download an install a recent version of R (4.0 or greater) at [https://www.r-project.org/][1], you can follow the [Bioconductor installation instructions][2] and get a workable environment fairly straightforwardly. I'd be happy to s ...
written 22 days ago by Rory Stark790
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Comment: C: Loading Sample Sheet in DiffBind
... Wow, are you sure? That is five years old and definitely no longer supported. What version of R are you running? Could you post the output of sessionInfo()? ...
written 22 days ago by Rory Stark790
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Comment: C: Loading Sample Sheet in DiffBind
... What version of `DiffBind` are you running? ...
written 23 days ago by Rory Stark790
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Comment: C: how matrix composition influences the final results in diff bind
... The update is now available in Bioconductor. Let me know if you have any more problems. FYI, next month a major update of DiffBind will be released, with much greater control over model designs, contrasts, normalization, and blacklists. ...
written 6 weeks ago by Rory Stark790
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Comment: C: how matrix composition influences the final results in diff bind
... I have checked in the fix. It will appear in DiffBind 2.16.1 once it gets through the Bioconductor build process (usually a day or two unless there is a problem). If you are able to install from source (ie on linux), I can send you the .tar.gz (2Mb). Cheers- Rory ...
written 6 weeks ago by Rory Stark790
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Comment: C: how matrix composition influences the final results in diff bind
... Francesca, thanks to you pointing out that it failed when you supplied the consensus peakset, but it worked when you let `DiffBind` compute the consensus, I was able to reproduce this and find the bug. I am working on a fix now and will post here when it is available. The workaround is to do it the ...
written 6 weeks ago by Rory Stark790
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Comment: C: how matrix composition influences the final results in diff bind
... I'll have a look at this later this afternoon to see if I can reproduce it. In the meantime if you are working on this now perhaps you could try the suggestion I made on the other thread? Try breaking the counting into two steps: dbObjprova <- dba.count(dbObjprova, peaks=consensus, summits ...
written 6 weeks ago by Rory Stark790
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Answer: A: how matrix composition influences the final results in diff bind
... Hello Francesca- There are a number of things that could account for this. Among other things, the consensus peakset will be different each time, which will change things a fair amount. Additionally, as you are not re-centering around summits, even if there are similar peaks in each version, they w ...
written 6 weeks ago by Rory Stark790
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Answer: A: Comparing peaks between multiple samples
... Yes you can do this. You can divide things up using any combination of meta-factors (Tissue, Factor, Condition, Treatment, Replicate), each of which can contain anything you like, or by calling out any subsets of peak using masks. Cheers- Rory ...
written 8 weeks ago by Rory Stark790

Latest awards to Rory Stark

Scholar 6 weeks ago, created an answer that has been accepted. For A: [How to Save plots in R] DiffBind
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Scholar 3 months ago, created an answer that has been accepted. For A: [How to Save plots in R] DiffBind
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
Scholar 2.4 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 2.7 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 3.0 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 3.1 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Scholar 3.1 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit

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