User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey230
Reputation:
230
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Trusted
Location:
Australia
Website:
http://www.peterhickey...
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PeteHaitch
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Google Scholar Page
Last seen:
6 days, 2 hours ago
Joined:
4 years, 8 months ago
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Posts by Peter Hickey

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Finding DMRs using dmrFinder in bsseq
... There were multiple warnings following bsseq.data.smoothed <- BSmooth(bsseq.data, verbose=TRUE). Did you look to see what there were? Above I suggested that because you are analysing RRBS data you would need to explore different parameters to BSmooth() but you've used the defaults. I suspect this ...
written 6 days ago by Peter Hickey230
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Answer: A: bsseq combineList: how to get an HDF5Array-backed object as return value?
... Hi Martin, combineList(hdf5_BS1, hdf5_BS2, BACKEND = "HDF5Array") will give you a HDF5Array-backed BSseq object. It's somewhat buried in the docs, but see ?combineList.  Currently, the default location for HDF5 files is specified via HDF5Array::setHDF5DumpDir(). You can check the current dump dir ...
written 21 days ago by Peter Hickey230
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Comment: C: Finding DMRs using dmrFinder in bsseq
... I am unable to reproduce the error. However, your example code has a bug: list.files(pattern="*.cov") -> cov.files means that the chr16 and chr20 data will be considered to have come from separate samples. This is not what you want. I tidied up and simplified your example code and was able to su ...
written 4 weeks ago by Peter Hickey230
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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 5 weeks ago by Peter Hickey230
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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 5 weeks ago by Peter Hickey230
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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 5 weeks ago by Peter Hickey230
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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 6 weeks ago by Peter Hickey230
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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 11 weeks ago by Peter Hickey230
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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 11 weeks ago by Peter Hickey230
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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 3 months ago by Peter Hickey230

Latest awards to Peter Hickey

Scholar 18 days ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 16 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 16 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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