Moderator: Kasper Daniel Hansen

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KasperDHansen
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Posts by Kasper Daniel Hansen

<prev • 723 results • page 1 of 73 • next >
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Comment: C: Combining pfilter (wateRmelon) and preprocessNoob (minfi)
... In minfi we have the function subsetByLoci() which might be useful in these situations. The issue is that an RGChannelSet is indexed by Addresses (kind of locations of the probes) while a MethylSet (and friends) is indexed by CpG names and we sometimes have multiple addresses <-> 1 CpG because ...
written 6 weeks ago by Kasper Daniel Hansen6.4k
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Answer: A: Conditional Quantile Normalization (cqn) error
... If you send me the input, I can take a slow look. Best, Kasper (Sent from my phone.) ...
written 3 months ago by Kasper Daniel Hansen6.4k
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Comment: C: [read.metharray] Trying to parse different IDAT files, of different size and ty
... If these are indeed the same arrays, but just with slightly different number of beads, then it should work. If not, then it shouldn't (Ie you cannot read in 450k and EPIC together). It is hard to know which case it is. If you want more help, you should make (some of) the idat files available on drop ...
written 3 months ago by Kasper Daniel Hansen6.4k
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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 months ago by Kasper Daniel Hansen6.4k
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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 5 months ago by Kasper Daniel Hansen6.4k
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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 7 months ago by Kasper Daniel Hansen6.4k
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Answer: A: Error using Conditional Quartile Normalization (CQN)
... What is the output of summary(GC_content[,1]) Best, Kasper ...
written 7 months ago by Kasper Daniel Hansen6.4k
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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 7 months ago by Kasper Daniel Hansen6.4k
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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 7 months ago by Kasper Daniel Hansen6.4k
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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 10 months ago by Kasper Daniel Hansen6.4k • updated 10 months ago by Martin Morgan ♦♦ 23k

Latest awards to Kasper Daniel Hansen

Popular Question 7 months ago, created a question with more than 1,000 views. For smoothing function in bumphunter in minfi
Great Question 10 months ago, created a question with more than 5,000 views. For Bioconductor on Coursera
Popular Question 10 months ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Popular Question 10 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Popular Question 10 months ago, created a question with more than 1,000 views. For using offsets from EDASeq and cqn for edgeR
Scholar 10 months ago, created an answer that has been accepted. For A: Illumina Methylation 27k minfi
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Views on BSgenome object
Popular Question 2.9 years ago, created a question with more than 1,000 views. For defaults in BiocParallel
Popular Question 2.9 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 3.5 years ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 3.5 years ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Scholar 3.5 years ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Appreciated 4.1 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 4.9 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 9.7 years ago, created 100 posts.

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