User: Gord Brown

gravatar for Gord Brown
Gord Brown590
Reputation:
590
Status:
Trusted
Location:
United Kingdom
Last seen:
8 months, 3 weeks ago
Joined:
6 years, 12 months ago
Email:
g***********@cruk.cam.ac.uk

Gord is a computational biologist / bioinformatician with Cancer Research UK's Cambridge Institute.  He works on pipeline and software infrastructure development, primarily on next-gen sequencing.

Posts by Gord Brown

<prev • 116 results • page 3 of 12 • next >
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Comment: C: DiffBind consensus peak help
... This tells us that DiffBind is indeed finding the difference extremely significant.  I'll have to leave it to Rory to understand what's happening with the output. ...
written 2.3 years ago by Gord Brown590
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Comment: C: DiffBind consensus peak help
... Thanks, that looks current, so the old bug shouldn't be a problem.  Unfortunately I can't see anything obvious.  The default for dba.count is minOverlap=2, so presence of a peak in two samples should be sufficient. Could you post or email your sample sheet?  And the results of printing the dba obje ...
written 2.3 years ago by Gord Brown590
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Answer: A: How to set the parameter "fragmentSize" in DiffBind and set parameter for paired
... Hi, EdgeR and DESeq2 use the same underlying statistical model, but they normalise quite differently, which accounts for most of the difference we see (and yes, we also see that they give very different answers in many cases).  if you look at the MA plots via dba.plotMA, you can usually see which o ...
written 2.4 years ago by Gord Brown590
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Answer: A: How to use Diffbind as complete beginner?
... DiffBind is an R package.  You can't expect to use it without a basic understanding of R.  If the vignette doesn't give you what you need, then you should consider taking an introductory R course.  Sorry, but there's no magic solution other than learning some R. ...
written 2.4 years ago by Gord Brown590
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Answer: A: DiffBind: failed to run dba.count in SSH
... Your sessionInfo() tells me that you're running an extremely old version of DiffBind, and R.  Your read bed files probably have 5 columns, which is not legal bed format (although it is the format some aligners will give you).  You need either 3 columns, or 6 or more.  Ideally, upgrade to the current ...
written 2.6 years ago by Gord Brown590
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Comment: C: DiffBind: failed to run dba.count in SSH
... Your sample sheet looks reasonable.  (Normally we'd store all the bam or bed or peak files in subdirectories called bam or bed or peak, so the sample sheet would have to include the full (or relative) paths to the files, but you would get a different error if it couldn't find the files at all.) Ple ...
written 2.6 years ago by Gord Brown590
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Answer: A: RStudio quits unexpectedly while running DiffBind on R 3.4.0
... Hi, Based on the data you provided offline, I reproduced and (eventually...) fixed the bug (buffer overflow).  It'll show up as DiffBind 2.4.2 (or 2.5.1 in the development branch) after the next build cycle of Bioconductor (usually a day or so). Thanks for reporting it. Cheers,  - Gord ...
written 2.6 years ago by Gord Brown590
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Comment: C: DiffBind: failed to run dba.count in SSH
... Hi, Could you post the output of "sessionInfo()" so we can see what version you're running?  There were bugs in earlier versions of DiffBind when using bed files for counts.  Just to clarify your comment, are your reads in .bed (or .bed.gz) format instead of .bam?  We used to support .bed for reads ...
written 2.6 years ago by Gord Brown590
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Comment: C: RStudio quits unexpectedly while running DiffBind on R 3.4.0
... Hi, FYI, I tried from within RStudio as well, and on our test data set, got no errors.  So I'd be very interested to see your data. Cheers,  - Gord ...
written 2.6 years ago by Gord Brown590
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Comment: C: Path to file in windows
... Hi, Well, the paths look right.  Your sessionInfo shows that your versions of R and DiffBind are close to 4 years out of date, though.  Could you upgrade to R 3.3.3 or 3.4.0 and try again?  We can't support versions of DiffBind that old. ...
written 2.6 years ago by Gord Brown590

Latest awards to Gord Brown

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 2.6 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Centurion 2.6 years ago, created 100 posts.
Scholar 2.6 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Scholar 4.1 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Counting Raw Reads with DiffBind
Scholar 4.7 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals
Autobiographer 4.8 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 5.1 years ago, created an answer that has been accepted. For A: DiffBind dba.plotVenn - Venn doesn't match Intervals

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