User: Peter Hickey

gravatar for Peter Hickey
Peter Hickey240
Reputation:
240
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Trusted
Location:
Johns Hopkins University, Baltimore, USA
Website:
http://www.peterhickey...
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PeteHaitch
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Google Scholar Page
Last seen:
2 days, 23 hours ago
Joined:
5 years ago
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Posts by Peter Hickey

<prev • 60 results • page 1 of 6 • next >
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Answer: A: BSmooth 'names' attribute must be the same length as the vector
... Hi Ravi, I have seen this error before when running on a cluster with a large value of mc.cores. Unfortunately, I don't know the exact cause (I suspect one of the jobs dies, possibly because it runs out of memory). I have been able to get around this by reducing to, say, mc.cores = 8. Does this wor ...
written 2 days ago by Peter Hickey240
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Comment: C: Error from scater package
... Please include the output of sessionInfo() in your question (http://www.bioconductor.org/help/support/posting-guide/) ...
written 6 days ago by Peter Hickey240
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Answer: A: Unusually long running times for getMeth function since latest release
... Thanks for your patience, Alejandro. I've committed a fix - it's available from https://github.com/PeteHaitch/bsseq. If you're able to, would you please give it a try to confirm that it fixes the performance regression. It requires that you are using Bioc-devel and can then be installed with BiocIns ...
written 3 months ago by Peter Hickey240
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Comment: C: Unusually long running times for getMeth function since latest release
... Hi Alejandro, Reproducible code and data would be appreciated. No need for it to be the full object, just enough for issue to be a noticeable drag on performance. Cheers, Pete On Fri., 30 Jun. 2017, 9:37 am Alejandro Reyes [bioc], < noreply@bioconductor.org> wrote: > Activity on a post ...
written 3 months ago by Peter Hickey240
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Comment: C: Unusually long running times for getMeth function since latest release
... I noticed this too but haven't had time to fix. I have an inkling of what's causing this and I'll try to fix over the weekend On Thu., 29 Jun. 2017, 5:48 pm Kasper Daniel Hansen [bioc], < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org & ...
written 3 months ago by Peter Hickey240
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Comment: C: Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this o
... Please include the result of running sessionInfo() to help diagnose the problem. Does it work if you load the object from command line R rather than from Rstudio?  ...
written 3 months ago by Peter Hickey240
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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 4 months ago by Peter Hickey240
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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 4 months ago by Peter Hickey240
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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 5 months ago by Peter Hickey240
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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 months ago by Peter Hickey240

Latest awards to Peter Hickey

Scholar 4 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 20 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq
Scholar 20 months ago, created an answer that has been accepted. For A: t-statistic cutoff for finding DMRs with bsseq

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