Moderator: Kasper Daniel Hansen

gravatar for Kasper Daniel Hansen
Reputation:
6,430
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Trusted
Location:
United States
Website:
http://www.hansenlab.org/
Twitter:
KasperDHansen
Scholar ID:
Google Scholar Page
Last seen:
3 months, 4 weeks ago
Joined:
13 years, 10 months ago
Email:
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Posts by Kasper Daniel Hansen

<prev • 720 results • page 1 of 72 • next >
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Answer: A: Exporting graphNEL into Cytoscape using RCy3 fails with 'arguments imply differi
... Just reading over the code, I am guessing that RCy3 has a problem with subgraphs? ...
written 5 weeks ago by Kasper Daniel Hansen ♦ 6.4k
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Answer: A: mini error in read.metharray
... If you're using read.metharray, the base names argument is a vector which is half the length of the number of files, equal to the number of samples. You need to remove the _Grn and _Red from the file names and remove any duplicates. read.metharray.exp() is probably an easier to use interface. ...
written 6 weeks ago by Kasper Daniel Hansen ♦ 6.4k
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Comment: C: Error using Conditional Quartile Normalization (CQN)
... Well, it shows that you do in fact have NA's in the length vector, contrary to what you said. You could remove those 25 genes or figure out what their length is and enter it into the GC_content object. Best, Kasper ...
written 3 months ago by Kasper Daniel Hansen ♦ 6.4k
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Answer: A: Error using Conditional Quartile Normalization (CQN)
... What is the output of summary(GC_content[,1]) Best, Kasper ...
written 3 months ago by Kasper Daniel Hansen ♦ 6.4k
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Answer: A: Illumina Methylation 27k minfi
... This bug is fixed in minfi 1.29.4 (devel) and 1.28.4 (release) which I have just committed. Assuming they build fine, they will be available in a few days from Bioconductor and immediately from the GitHub page. Thanks for the report and the diagnose. Best, Kasper ...
written 3 months ago by Kasper Daniel Hansen ♦ 6.4k
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Comment: C: Reading 450k data in minfi
... The content you posted is the array design, not the actually measurements. You should not have to read this file in. ...
written 3 months ago by Kasper Daniel Hansen ♦ 6.4k
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Comment: C: Rgraphviz installation from source on Linux (Fedora 28) w BioC 3.8 -- failure
... This is a very weird error (missing XXX_pow_finite). We have confirmed that this arises when you use -O3 optimization which GCC 8 (or newer). The solution to this issue is to downgrade the optimization. The solution I intent to implemented (but slipped off my todo list) is to modify the configure sc ...
written 6 months ago by Kasper Daniel Hansen ♦ 6.4k • updated 6 months ago by Martin Morgan ♦♦ 23k
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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 6 months ago by Kasper Daniel Hansen ♦ 6.4k
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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 6 months ago by Kasper Daniel Hansen ♦ 6.4k
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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 9 months ago by Kasper Daniel Hansen ♦ 6.4k

Latest awards to Kasper Daniel Hansen

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Views on BSgenome object
Popular Question 2.5 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 2.5 years ago, created a question with more than 1,000 views. For defaults in BiocParallel
Scholar 3.2 years ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 3.2 years ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 3.2 years ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Popular Question 3.2 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Appreciated 3.8 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Scholar 4.5 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 9.4 years ago, created 100 posts.
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