Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

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Comment: C: Rgraphviz installation fails in R with OpenBLAS
... Peter, I took a more careful look at your report. Are the two different R installations (with and without OpenBLAS) compiled with different compilers?  I know that Rgraphviz fails using GCC 8 with -O3 optimization flags, with this particular error (missing `***__pow_finite`). You don't mention in y ...
written 10 days ago by Kasper Daniel Hansen6.4k
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Comment: C: Rgraphviz installation fails in R with OpenBLAS
... First a clarification. Version 2.26 is the Rgraphviz version 2.28 is the Graphviz versioon they have nothing to do with each other, although now that 26 ~ 28 it looks weird. Second, I figured out what the issue is, but I dropped the ball in fixing it. On Wed, Nov 28, 2018 at 9:45 AM mmokrejs [ ...
written 11 days ago by Kasper Daniel Hansen6.4k
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Answer: A: Taking relatedness among individuals into account in differential methylation an
... At first, I would use "standard" tools from GWAS to do this (not saying this is easy), either on data in the unit interval or the logit transformation. In principle all you need is a mixed effect model where the covariance matrix reflects the relatedness structure. On Sat, Aug 25, 2018 at 12:34 AM ...
written 3 months ago by Kasper Daniel Hansen6.4k
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Comment: C: annotationhub: data update
... In this case, this is an interface to a UCSC resource which I believe is provided by the core team (I could be wrong though). The implications (to me) is that as time goes on, the AnnotationHub version of the resource deviates from UCSC. I understand short term deviations in the sense that UCSC ha ...
written 3 months ago by Kasper Daniel Hansen6.4k
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annotationhub: data update
... If I run the following code to get RefSeq from UCSC: library(AnnotationHub) ahub <- AnnotationHub() ahub <- subset(ahub, species == "Homo sapiens" & genome == "hg19") query(ahub, "refseq")[1] I see > query(ahub, "refseq")[1] AnnotationHub with 1 record # snapshotDate(): 2018-08-01 ...
annotationhub written 3 months ago by Kasper Daniel Hansen6.4k • updated 3 months ago by shepherl ♦♦ 890
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Comment: C: Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
... Its a tough one. From the density plot it is a bit of an outlier which is never a good sign. On the other hand, the density per se does not look horrible. I would say it requires more information On Wed, Jul 25, 2018 at 10:54 PM peter.fransquet [bioc] < noreply@bioconductor.org> wrote: > ...
written 4 months ago by Kasper Daniel Hansen6.4k
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Answer: A: getSex error even when sex is provided
... This could well be a bug. Does it work if you just run your data through preprocessQuantile? Best, Kasper On Wed, Jun 20, 2018 at 3:13 PM, fgc [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User fgc <https: suppor ...
written 5 months ago by Kasper Daniel Hansen6.4k
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Answer: A: Problem installing Minfi on Cluster
... You have set up your R installation to use MKL, but you have not done it correctly. You need to sort this out with a sysadmin. You could benefit from consulting the R installation manual. This is something you need to fix at the R installation level (I think, unless you have local overrides). Kas ...
written 7 months ago by Kasper Daniel Hansen6.4k
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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 9 months ago by Kasper Daniel Hansen6.4k
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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 9 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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