Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.3k
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Posts by Kasper Daniel Hansen
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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 6 weeks ago by
Kasper Daniel Hansen ♦ 6.3k
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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 7 weeks ago by
Kasper Daniel Hansen ♦ 6.3k
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... Have you checked whether your system is current by running
biocValid()
...
written 10 weeks ago by
Kasper Daniel Hansen ♦ 6.3k
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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 3 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 3 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 6 months ago by
Kasper Daniel Hansen ♦ 6.3k
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754
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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 6 months ago by
Kasper Daniel Hansen ♦ 6.3k
0
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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 6 months ago by
Kasper Daniel Hansen ♦ 6.3k
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444
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... Its the same issue. When you get intensities only from GEO you do not get
- control probes
- out of band probes
To get this information, you generally need the original IDAT files. This means that any algorithm which makes use of either control probes or out of band probes will fail.
...
written 6 months ago by
Kasper Daniel Hansen ♦ 6.3k
0
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652
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Comment:
C: Rgraphviz installation fails
... You should do
# env | grep usr/lib
to see what is being set. You could also try to have a look at
# R CMD config CFLAGS
# R CMD config LDFLAGS
Comparing to the build report, which has the following invocation:
/bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -Wall -module
-avoid-version ...
written 8 months ago by
Kasper Daniel Hansen ♦ 6.3k
Latest awards to Kasper Daniel Hansen
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For support for EPIC methylation arrays in minfi
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Minfi User Guide Build Problem?
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: Covert MethylSet to RGChannelSet object
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Bioconductor on Coursera
Scholar
3.4 years ago,
created an answer that has been accepted.
For A: QC/normalization standards for cancer studies with 450k array data
Centurion
8.2 years ago,
created 100 posts.
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