User: Rory Stark
Rory Stark • 600
- 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 >
1
vote
1
answer
85
views
1
answers
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 Stark • 600
0
votes
1
answer
93
views
1
answers
... 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 Stark • 600
0
votes
1
answer
329
views
1
answers
... 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 Stark • 600
2
votes
1
answer
502
views
1
answers
... 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 Stark • 600
0
votes
1
answer
344
views
1
answers
... 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 Stark • 600
0
votes
1
answer
208
views
1
answers
... 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 Stark • 600
0
votes
2
answers
632
views
2
answers
...
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 Stark • 600
1
vote
0
answers
1.8k
views
0
answers
... 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 Stark • 600
0
votes
1
answer
510
views
1
answers
... The DiffBind package in Bioconductor creates a read count matrix from peak calls and aligned reads. ...
written 20 months ago by
Rory Stark • 600
1
vote
1
answer
878
views
1
answers
... 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 Stark • 600
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
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Appreciated
20 months ago,
created a post with more than 5 votes.
For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
Appreciated
22 months ago,
created a post with more than 5 votes.
For A: Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal Wit
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
Appreciated
2.1 years ago,
created a post with more than 5 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
Appreciated
4.5 years ago,
created a post with more than 5 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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 926 users visited in the last hour