User: Rory Stark

gravatar for Rory Stark
Rory Stark410
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410
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Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Last seen:
2 days, 19 hours ago
Joined:
4 years, 1 month ago
Email:
r*********@cruk.cam.ac.uk

Posts by Rory Stark

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Diffbind - Very high proportion of significant peaks
... I have certainly see this level of differentially Some questions: - Do you expect the conditions to change the open chromatin landscape quite a bit? - How are the differential sites divided between the two conditions? Do they mostly show increases in one condition, or are there many ch ...
written 6 weeks ago by Rory Stark410
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Answer: A: Diffbind error : sequences from an unspecified genome; no seqlengths
... Has this been resolved? You shouldn't need to specify the genome as DiffBind takes the chromosome names directly from the peak files, so if they are consistent it should work. However there was a bug at some point that impacted this in certain cases. What version of DiffBind are you using? Alterna ...
written 6 weeks ago by Rory Stark410
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Answer: A: What is the best method ChIPseq differential binding analysis?
... Disclosure: I am the author of `DiffBind`, a differential binding analysis tool. Interestingly, the tools you are considering are not the ones most often used to derive results in the published literature. `MACS` + `DiffBind` is by far the most widely used combo for experiments with multiple biolog ...
written 3 months ago by Rory Stark410
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Comment: C: DiffBind - Erroneous Affinity Shift In One Direction
... Can you confirm which version you are using from `sessionInfo()`? I'm limited in what I can do without examining the object, but here's a few things to look at. Something is going on in counting the A sample peaks. Look at them un-normalized (`bNormalized=FALSE`). If they are all 1 then nothing is ...
written 3 months ago by Rory Stark410
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Answer: A: DiffBind - Erroneous Affinity Shift In One Direction
... Hello, I am the author of `DiffBind`. 1) There are a number of things that could account for the A-B differences. You say all the shifts are in one direction, which I assume means that the fold-changes of all the differentially bound (DB) sites have the same sign? It may be instructive to look at t ...
written 3 months ago by Rory Stark410
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Answer: A: Diffbind package DESeq2 analysis
... The most obvious answer would be that there may not be any significantly deferentially bound peaks in your experiment. This could be due to the biology (nothing is changing) or be related to the experimental design. For example, the experiment could be underpowered, mostly likely due to not having e ...
written 4 months ago by Rory Stark410
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Answer: A: Huge difference between differential peaks with EdgeR and DESeq2 using Diffbind
... I suspect you are actually correct in your initial suspicion that the difference is in normalization. We most often see this behavior when there is a lot more signal in one sample group than the other. You can check for this by comparing three plots: > par(mfrow=c(3,1)) > dba.plotMA( ...
written 7 months ago by Rory Stark410
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Answer: A: [How to Save plots in R] DiffBind
... The comment above is the correct answer to the question. Before plotting, call one of the functions that redirects the plot to a file, such as `jpeg()`, `pdf()`, or `png()`. After plotting, call `dev.off()` to close the file. You can do multiple plots before calling `dev.off()` and they will all end ...
written 7 months ago by Rory Stark410
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Answer: A: Visualization for ChIP-seq analysis
... If you have a lot of samples (including replicates), it can be very useful to visualize sample clustering. Examples include heatmaps with hierarchical clustering and PCA. The [DiffBind package in Bioconductor][1] provides clustering and PCA plots, as well as MA, box, and volcano plots after performi ...
written 7 months ago by Rory Stark410
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Answer: A: Convert DiffBind output to standard BED or NarrowPeak format
... You can generate bed files from a `GRanges` object (as returned by `dba.report`) using `export.bed()` from the `rtracklayer` package. > library(rtracklayer) > dbsites <- dba.report(myDBA, contrast=1, th=0.05) > export.bed(dbsites,"dbsites.bed") ...
written 7 months ago by Rory Stark410

Latest awards to Rory Stark

Teacher 4 weeks 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 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 3 months 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 7 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 7 months ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
Teacher 7 months 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 7 months ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 7 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 7 months 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 8 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 8 months 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 2.7 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
Popular Question 3.6 years ago, created a question with more than 1,000 views. For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
Appreciated 4.0 years ago, created a post with more than 5 votes. For ChIPQC: a package for assessing quality of ChIP-seq samples and experiments

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