Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 713 results • page 2 of 72 • next >
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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 months ago by Kasper Daniel Hansen6.4k
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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 11 months ago by Kasper Daniel Hansen6.4k
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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 11 months ago by Kasper Daniel Hansen6.4k
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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 13 months ago by Kasper Daniel Hansen6.4k
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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 13 months ago by Kasper Daniel Hansen6.4k
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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 13 months ago by Kasper Daniel Hansen6.4k
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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 14 months ago by Kasper Daniel Hansen6.4k
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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 15 months ago by Kasper Daniel Hansen6.4k
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Comment: C: Rgraphviz installation fails
... You're using the bundled Graphviz, so the fact you have it installed in your system shouldn't matter. This looks weird: /bin/bash ./libtool --tag=CC --mode=link gcc -std=gnu99 -g -O2 -module -avoid-version -L/usr/local/lib64 -L-L/usr/lib/ -ltcl8.6 -L/usr/lib/ -ltk8.6 -ldl -o dlopen.la dlopen. ...
written 15 months ago by Kasper Daniel Hansen6.4k
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Comment: C: Rgraphviz installation fails
... You don't need to install Graphviz yourself, it is bundled with Rgraphviz. What is the beginning of the Rgraphviz installation output and what command (exactly) do you use to install it? ...
written 15 months ago by Kasper Daniel Hansen6.4k

Latest awards to Kasper Daniel Hansen

Popular Question 24 months ago, created a question with more than 1,000 views. For Views on BSgenome object
Popular Question 24 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 24 months ago, created a question with more than 1,000 views. For defaults in BiocParallel
Scholar 2.7 years ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 2.7 years ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Popular Question 2.7 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Appreciated 3.2 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Scholar 4.0 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 8.9 years ago, created 100 posts.

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