User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey210
Reputation:
210
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Trusted
Location:
Australia
Website:
http://www.peterhickey...
Twitter:
PeteHaitch
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Google Scholar Page
Last seen:
17 hours ago
Joined:
4 years, 7 months ago
Email:
p***********@gmail.com

Posts by Peter Hickey

<prev • 51 results • page 1 of 6 • next >
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Comment: C: Finding DMRs using dmrFinder in bsseq
... Thanks, Nastasia. Can you please also post the exact command you ran that worked for chr20 but not for chr16 ...
written 17 hours ago by Peter Hickey210
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Comment: C: Finding DMRs using dmrFinder in bsseq
... It's difficult to know what's causing the error from that output. Are you able to share the chr16 data with me (e.g., via Dropbox)? I could then investigate further ...
written 3 days ago by Peter Hickey210
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Comment: C: Finding DMRs using dmrFinder in bsseq
... 1. Setting ns so large is probably not a good idea for RRBS data. As documented, ns is the minimum number of methylation loci in a smooth window. Most RRBS captured regions will contain many, many fewer CpGs, so you will be smoothing over large windows containing several clusters of CpGs with large ...
written 7 days ago by Peter Hickey210
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Answer: A: Finding DMRs using dmrFinder in bsseq
... To answer some of your specific questions: 1. The warnings generated during BSmooth() are coming from the underlying locfit R package. Such warnings are quite technical by nature and can be hard to understand, but they often indicate a problem with the choice of smoothing parameters. The default BS ...
written 7 days ago by Peter Hickey210
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Comment: C: BSmooth error during the smoothing step for a subset of files
... I'm currently exploring parameter choices for non-CG loci, but in human. I recognise that non-CG loci are prevalent and important for methylation in plants and that it would be good to provide recommendations. The simple reason we don't is because neither Kasper (main developer) nor myself analyse p ...
written 6 weeks ago by Peter Hickey210
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Answer: A: BSmooth error during the smoothing step for a subset of files
... Hi Brandon, This issue is that the default BSmooth() parameters, especially ns, h, and maxgap, are tuned for the distribution of CG loci in human/mammalian genomes [1]. You are using these default parameters to analyse CHH loci from what I'm guessing is soybean (based on 'Gm01' in your example), an ...
written 6 weeks ago by Peter Hickey210
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Comment: C: BSmooth error during the smoothing step for a subset of files
... Thanks, Brandon. I was able to reproduce the error using the BS1.12M.CHH.gz file. Ultimately, an error is occurring when locfdr::locfit() is called from within bsseq::BSmooth(). Unfortunately, because it's a little buried and calling some fairly complicated code in locfdr, this means it will take a ...
written 8 weeks ago by Peter Hickey210
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Comment: C: BSmooth error during the smoothing step for a subset of files
... Hi Brandon, Can you produce and share a minimal CHH file that reproduces the error? I've not had issues specific to CHH files. Cheers, Pete ...
written 8 weeks ago by Peter Hickey210
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Comment: C: Aclust package: IlluminaHumanMethylation450kCHR37 not found
... Jim's covered your main options. Just adding that I haven't tried to use Aclust in quite some time and don't have a version with proper 450k annotation support nor do I plan to make one. It sounds like you've come across this, but in case you haven't, Brent Pedersen re-implemented the Aclust algori ...
written 9 months ago by Peter Hickey210
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Comment: C: Unable to load/install rtracklayer (v1.33.2) on OS X (possibly SSL-related?)
... Wonderful, that fixed it. Installed from Bioconductor-mirror github repo (without setting DYLD_LIBRARY_PATH or modifying my default openssl or PATH). Thanks for your help, Michael. ...
written 11 months ago by Peter Hickey210

Latest awards to Peter Hickey

Scholar 15 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 15 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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