Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

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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 27 days 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 27 days 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 27 days 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 weeks 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 12 weeks ago by Kasper Daniel Hansen6.3k
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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 12 weeks ago by Kasper Daniel Hansen6.3k
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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 3 months ago by Kasper Daniel Hansen6.3k
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Comment: C: ChAMP filter removing good samples from different batch of EPIC arrays.
... The many failed samples is because the data from these (later) arrays are scrambled and therefore garbage. This happens when you read epic arrays which have different number of probes in, with earlier versions of minfi. This is fixed in current release. Best, Kasper (Sent from my phone.) > On A ...
written 3 months ago by Kasper Daniel Hansen6.3k
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Answer: A: minfi - error when reading idat files
... This looks good to me. You don't get an error with force=TRUE. What you're seeing is that you have two sets of IDAT files scanned with different scan settings (specifically with different DMAP files). We see this a lot with the EPIC array. It is unfortunate that Illumina has released some many D ...
written 4 months ago by Kasper Daniel Hansen6.3k
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Comment: C: support for EPIC methylation arrays in minfi
... The latest stable version is 1.22.1. You should update R and Bioconductor. On Fri, Jun 30, 2017 at 3:55 AM, r.clifford [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User r.clifford <https: support.bioconductor.org ...
written 4 months ago by Kasper Daniel Hansen6.3k

Latest awards to Kasper Daniel Hansen

Popular Question 19 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 19 months ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 19 months ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 19 months ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Appreciated 2.2 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 2.9 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.8 years ago, created 100 posts.

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