User: Rory Stark

gravatar for Rory Stark
Rory Stark380
Reputation:
380
Status:
Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Last seen:
4 days, 1 hour ago
Joined:
3 years, 10 months ago
Email:
r*********@cruk.cam.ac.uk

Posts by Rory Stark

<prev • 15 results • page 1 of 2 • next >
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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 16 days ago by Rory Stark380
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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 28 days ago by Rory Stark380
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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 28 days ago by Rory Stark380
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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 6 weeks ago by Rory Stark380
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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 4 months ago by Rory Stark380
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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 4 months ago by Rory Stark380
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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 4 months ago by Rory Stark380
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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 4 months ago by Rory Stark380
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Answer: A: How many biological replicates needed for ChIP seq experiments?
... It depends on what questions you are trying to answer with your ChIP-seq experiments. The two-replicate guideline applies only to **identification of binding sites** ("site discovery"). This is a binary determination (binding-site vs. not-a-binding-site), potentially with an associated confidence s ...
written 5 months ago by Rory Stark380
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Answer: A: Converting narrowPeak to bed
... `DiffBind` supports `narrowPeak` format directly, Just specify "`narrow`" as the value for `PeakCaller` in your samplesheet. -Rory ...
written 5 months ago by Rory Stark380

Latest awards to Rory Stark

Scholar 16 days ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 16 days 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 4 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 4 months ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
Teacher 4 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 4 months ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 4 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 4 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 5 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 5 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 2.4 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
Popular Question 3.3 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 3.8 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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