User: Rory Stark

gravatar for Rory Stark
Rory Stark600
Reputation:
600
Status:
Trusted
Location:
University of Cambridge, Cancer Research UK - Cambridge Institute
Last seen:
22 hours ago
Joined:
5 years, 11 months ago
Email:
r*********@cruk.cam.ac.uk

Posts by Rory Stark

<prev • 29 results • page 1 of 3 • next >
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Answer: A: Diffbind-edgeR or Deseq2
... Usually when ther eis a big difference between the edgeR and DESeq2, it is driven by differences in normalization. This is generally due to an experiment where there is a wholesale change in binding patterns between two conditions, generally in one direction. The TMM normalization used in edgeR assu ...
written 17 days ago by Rory Stark600
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Answer: A: Calculate correlations between ChipSeq data sets
... The `DiffBind` package in `Bioconductor` will calculate correlation values and plot clustered correlation heatmaps (as well as PCA plots, which are are useful to assess similarity amongst ChIP-seq samples). This works by looking at all the peaks (called by MACS2 in your case), forming a consensus s ...
written 29 days ago by Rory Stark600
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Answer: A: Which method is the best for using in "dba.count" in Diffbind R package
... One important thing to note is that the score computed by `dba.count()` is only used for plotting the entire binding matrix. The values used for the differential analysis (using `dba.analyze()`) are determined at analysis time based on the values of certain parameters (`method`, `bSubControl`, and ...
written 5 months ago by Rory Stark600
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Answer: A: Are MACS2's summit or DiffBind's summit options are recommended for histone mark
... Yes, I would use the summits option in DiffBind to analyze these data. This is straightforward for the H3K4me3 mark, which is generally narrow. For the other marks, which tend to be enriched over a wider intervals, generally the important thing is to accurately detect changes in enrichment in the ...
written 6 months ago by Rory Stark600
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Answer: A: DiffBind package showing warnings and unable to analyse my data
... What are the sample groups that you are trying to find the difference between? If all four samples are replicates of the same sample type, there is nothing to contrast. Another way to look at this: if all the samples have the same values for the Condition, what other attribute (Tissue, Factor, Tre ...
written 8 months ago by Rory Stark600
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Answer: A: Diffbind affinity based analysis
... It is most certainly possible for the quantitative (affinity) analysis to be unable to identify differentially bound sites, even when there are peaks called only in one condition. There are a number of reasons why this can occur. First, there may be a number of borderline peaks that are above the ...
written 10 months ago by Rory Stark600
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Answer: A: how to retrieve binding affinity matrix in diffbind
... dba.peakset(myDBA, bRetrieve=TRUE, writeFile="BindingAffinityMatrix.csv") The values will be the score used in `dba.count()`, the default is `DBA_SCORE_TMM_MINUS_FULL` (TMM normalised read counts after subtracting control reads, based on the number of reads in each bam file). To get, for exam ...
written 12 months ago by Rory Stark600
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Comment: C: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' lengt
... I am the package maintainer for DiffBind. If you send a copy of (or link to) the DBA object `results` I can troubleshoot it for you. My email is in the DiffBind documentation. -Rory ...
written 12 months ago by Rory Stark600
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Answer: A: create a RC matrix with narrowPeak data
... The DiffBind package in Bioconductor creates a read count matrix from peak calls and aligned reads. ...
written 20 months ago by Rory Stark600
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Answer: A: How to correlate chip seq peaks?
... I'm not sure how two peaks could be considered "similar" if their locations are several kb apart? We usually think of peaks being the same in replicates if their coordinates at least overlap. That said, a very easy way to get pearson or spearman correlation values is to read all the peaksets into t ...
written 20 months ago by Rory Stark600

Latest awards to Rory Stark

Good Answer 19 days 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 5 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 5 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 22 months ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 22 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 23 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 2.2 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Teacher 2.2 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 2.5 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Visualization for ChIP-seq analysis
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
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How many biological replicates needed for ChIP seq experiments?
Scholar 2.5 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
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 2.5 years ago, created an answer that has been accepted. For A: How many biological replicates needed for ChIP seq experiments?
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
Teacher 4.5 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
Popular Question 5.4 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 5.9 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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