Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 675 results • page 1 of 68 • next >
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Comment: C: support for EPIC methylation arrays in minfi
... Could you copy and paste code + error. Best, Kasper (Sent from my phone.) > On Feb 22, 2017, at 12:05, paularl3773 [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User paularl3773 wrote Comment: support for EPIC met ...
written 10 hours ago by Kasper Daniel Hansen6.2k
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Answer: A: BSmooth: mclapply error when smoothing using BSmooth
... That is weird. How many samples do you have? On Tue, Jan 17, 2017 at 12:02 PM, zuupcat [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User zuupcat <https: support.bioconductor.org="" u="" 12187=""/> wrote Questio ...
written 5 weeks ago by Kasper Daniel Hansen6.2k
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Answer: A: MINFI missing samples in qcreports and densityplots
... Look at the pheno object; perhaps there are missing values? On Fri, Jan 6, 2017 at 2:47 PM, annabelle.congras [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User annabelle.congras <https: support.bioconductor.org=" ...
written 6 weeks ago by Kasper Daniel Hansen6.2k
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Comment: C: bumphunter output clarification
... A cluster is defined purely based on the array design (the spacing between probes). It is a collection of probes where the between probe distance (on the genome) is smaller than X. If X is set to be Inf, each chromosome will be a cluster. A region is (always) a subset of a cluster and is a set of ...
written 6 weeks ago by Kasper Daniel Hansen6.2k
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Answer: A: minfi preprocessQuantile problem
... I have now fully analyzed the issue.  The problem is indeed caused by the bugfix introduced in minfi 1.20.0.  The version of preprocesQuantile in minfi 1.20.0 and 1.21.0-1.21.2 is wrong and should not be used. I have reverted the change and committed this to minfi 1.21.3 in the devel branch.  Follo ...
written 10 weeks ago by Kasper Daniel Hansen6.2k
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Answer: A: minfi preprocessQuantile problem
... Ok, I have looked into this, and I am not done yet.  I can replicate this problem with the data in `minfiData`, and it is indeed related to the bugfix introduced in preprocessQuantile().  I have (for now) added a `method` argument to preprocessQuantile in minfi 1.21.3 (right now only on Github); wit ...
written 10 weeks ago by Kasper Daniel Hansen6.2k
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Answer: A: minfi preprocessQuantile problem
... The bug should not have that effect.  For example, we re-checked some of the plots in the minfi paper and concluded they were unchanged. But it sounds worrisome.  Could you perhaps share some of the data; perhaps there is a smaller subset which shows this behaviour?  It is unfortunately basically i ...
written 11 weeks ago by Kasper Daniel Hansen6.2k
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email replies to support questions
... Recently (might be a at least for the past several weeks), replies to an emailed support question bounces.  That didn't use to be the case.  This is irritating, I have no idea when it happened. I'm using gmail, and I have just checked that the email at the support site is the correct one. ```` Del ...
support site written 11 weeks ago by Kasper Daniel Hansen6.2k • updated 10 weeks ago by gregory.wargula ♦♦ 30
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Comment: C: Error with Minfi while using read.metharray.exp() and read.metharray function
... each combination of (Array, Slide) should occur only once, because they represent a specific array. There are two files per array (one red and one green) but you should only have 1 row in the targets object. On Thu, Nov 10, 2016 at 3:02 PM, hrishi27n [bioc] <noreply@bioconductor.org> wrote: ...
written 3 months ago by Kasper Daniel Hansen6.2k
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Answer: A: Error with Minfi while using read.metharray.exp() and read.metharray function
... You most likely have duplicate rows in the targets. Could you show us a printout of that? Best, Kasper (Sent from my phone.) > On Nov 10, 2016, at 14:14, hrishi27n [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > Use ...
written 3 months ago by Kasper Daniel Hansen6.2k

Latest awards to Kasper Daniel Hansen

Popular Question 10 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 10 months ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 10 months ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 10 months ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Appreciated 17 months ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 17 months ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 2.2 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.1 years ago, created 100 posts.

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