Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 706 results • page 2 of 71 • next >
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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 9 months 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 9 months 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 9 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 10 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 11 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 11 months ago by Kasper Daniel Hansen6.3k
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Answer: A: Unusually long running times for getMeth function since latest release
... This should not happen, but clearly it does. We could use (a lot) more information about what is going on, including the length of the BSseq object and the ranges. Could you perhaps post this as an issue on our Github page. What is the backend of the BSseq object? Best, Kasper On Thu, Jun 29, 20 ...
written 11 months ago by Kasper Daniel Hansen6.3k
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Comment: C: support for EPIC methylation arrays in minfi
... Yes it is. What version of minfi are you using? Best, Kasper On Thu, Jun 29, 2017 at 5:23 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="" u="" 12781 ...
written 11 months ago by Kasper Daniel Hansen6.3k
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Answer: A: FuntooNorm on 450K and Epic data combined RGSet
... The authors of funtooNorm should modify their code to work with subsetted objects. This is something we now fully support in minfi and they can look in minfi to see examples of how to write it. One advantage of working with subsetted objects is to allow things like this. Best, Kasper On Tue, Jun ...
written 12 months ago by Kasper Daniel Hansen6.3k
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Comment: C: bsseq combineList: how to get an HDF5Array-backed object as return value?
... We should make this (and other) function(s) auto-guess the backend of the output. Obv. the default when input is all HDF5 should be HDF5 and likewise if all input is in-memory matrices. Should have capability of overriding of course. On Sat, Jun 10, 2017 at 1:20 AM, Martin Aryee [bioc] < norepl ...
written 12 months ago by Kasper Daniel Hansen6.3k

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
Appreciated 2.8 years ago, created a post with more than 5 votes. 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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