Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.3k
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Posts by Kasper Daniel Hansen
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... This could well be a bug.
Does it work if you just run your data through preprocessQuantile?
Best,
Kasper
On Wed, Jun 20, 2018 at 3:13 PM, fgc [bioc] <noreply@bioconductor.org>
wrote:
> Activity on a post you are following on support.bioconductor.org
>
> User fgc <https: suppor ...
written 4 days ago by
Kasper Daniel Hansen ♦ 6.3k
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... You have set up your R installation to use MKL, but you have not done it
correctly. You need to sort this out with a sysadmin. You could benefit
from consulting the R installation manual. This is something you need to
fix at the R installation level (I think, unless you have local overrides).
Kas ...
written 8 weeks ago by
Kasper Daniel Hansen ♦ 6.3k
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Comment:
C: Libgomp error in IHW
... We have been using the package successfully quite a few times, so I don't think it is a basic issue. It could depend on this exact set of p-values. I think we have a LOT of p-values for this application, but I will let Kipper speak to the details here.
...
written 3 months ago by
Kasper Daniel Hansen ♦ 6.3k
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Comment:
C: cpgCollapse in Minfi
... Thanks for answering this. Two points
1) The point of cpgCollapse is essentially to group CpGs into units. By
design each unit may contain >1 CpG so its not really possible to use the
name.
2) The name cgXXXXX is in fact informative. According to Illumina, the
XXXXX is a hash of the local seq ...
written 3 months ago by
Kasper Daniel Hansen ♦ 6.3k
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... Have you checked whether your system is current by running
biocValid()
...
written 4 months ago by
Kasper Daniel Hansen ♦ 6.3k
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Comment:
C: Rgraphviz installation fails
... I have a hard time fully understanding your message, but it seems to me
that you're saying everything works now?
Best,
Kasper
On Wed, Jan 10, 2018 at 7:05 AM, Giovanni Calice [bioc] <
noreply@bioconductor.org> wrote:
> Activity on a post you are following on support.bioconductor.org
> ...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.3k
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... The number of probes inside an IDAT file depends on the settings of the
scanner at the time of the scanning of the file. This is encaptured in a
so-called DMAP file. Unfortunately, Illumina has releaed multiple DMAP
files for the EPIC chip so it is quite standard to see what you see. This
was never ...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.3k
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... Suggestion on how to make all of this more robust would be great; happy to
make more checks. Perhaps file an issue on GitHub.
On Wed, Oct 25, 2017 at 7:20 AM, Andy91 [bioc] <noreply@bioconductor.org>
wrote:
> Activity on a post you are following on support.bioconductor.org
>
> User ...
written 8 months ago by
Kasper Daniel Hansen ♦ 6.3k
0
votes
1
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808
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... What is the output of
annotation(rgSet_blood)
sessionInfo()
(last one after the error). When did you create this rgSet - a long time
ago, recently or just now?
Best,
Kasper
On Wed, Oct 25, 2017 at 6:12 AM, poojitha.stemcell [bioc] <
noreply@bioconductor.org> wrote:
> Activity on a ...
written 8 months ago by
Kasper Daniel Hansen ♦ 6.3k
0
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1
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296
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... your zero-coverage sounds weird.
On Tue, Oct 24, 2017 at 10:34 PM, ravi.tharakan [bioc] <
noreply@bioconductor.org> wrote:
> Activity on a post you are following on support.bioconductor.org
>
> User ravi.tharakan <https: support.bioconductor.org="" u="" 14221=""/> wrote Comm ...
written 8 months ago by
Kasper Daniel Hansen ♦ 6.3k
Latest awards to Kasper Daniel Hansen
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Views on BSgenome object
Popular Question
18 months ago,
created a question with more than 1,000 views.
For support for EPIC methylation arrays in minfi
Popular Question
18 months ago,
created a question with more than 1,000 views.
For defaults in BiocParallel
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Minfi User Guide Build Problem?
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Covert MethylSet to RGChannelSet object
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For support for EPIC methylation arrays in minfi
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Bioconductor on Coursera
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: QC/normalization standards for cancer studies with 450k array data
Centurion
8.4 years ago,
created 100 posts.
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