User: Peter Hickey
Peter Hickey • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- Johns Hopkins University, Baltimore, USA
- Website:
- http://www.peterhickey...
- Twitter:
- PeteHaitch
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 days, 23 hours ago
- Joined:
- 5 years ago
- Email:
- p***********@gmail.com
Posts by Peter Hickey
<prev
• 60 results •
page 1 of 6 •
next >
0
votes
2
answers
45
views
2
answers
... 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 Hickey • 240
0
votes
1
answers
51
views
1
answers
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 Hickey • 240
0
votes
2
answers
154
views
2
answers
... 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 Hickey • 240
0
votes
2
answers
154
views
2
answers
... 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 Hickey • 240
0
votes
2
answers
154
views
2
answers
... 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 Hickey • 240
0
votes
1
answers
780
views
1
answers
... 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 Hickey • 240
0
votes
3
answers
279
views
3
answers
... 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 Hickey • 240
0
votes
1
answers
159
views
1
answers
... 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 Hickey • 240
0
votes
3
answers
279
views
3
answers
... 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 Hickey • 240
0
votes
3
answers
279
views
3
answers
... 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 Hickey • 240
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 289 users visited in the last hour