Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 705 results • page 1 of 71 • next >
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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 6 weeks ago by Kasper Daniel Hansen6.3k
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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 7 weeks ago by Kasper Daniel Hansen6.3k
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Comment: C: Minfi read.metharray error in checkslotassignment
... Have you checked whether your system is current by running  biocValid() ...
written 10 weeks ago by Kasper Daniel Hansen6.3k
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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 3 months ago by Kasper Daniel Hansen6.3k
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Answer: A: IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
... 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 Hansen6.3k
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Comment: C: Error using read.metharray.exp in minfi to read idat files
... 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 Hansen6.3k
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Comment: C: minfi - estimatecellcount function
... 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 Hansen6.3k
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Comment: C: BSmooth 'names' attribute must be the same length as the vector
... 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 Hansen6.3k
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Comment: C: Is it possible to convert Methylumi object into RGChannelSet
... 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 Hansen6.3k
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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 Hansen6.3k

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
Appreciated 2.6 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
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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