Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 674 results • page 1 of 68 • next >
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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 1 day 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 12 days 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 12 days 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 5 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 5 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 6 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 6 weeks ago by Kasper Daniel Hansen6.2k • updated 5 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 9 weeks 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 9 weeks ago by Kasper Daniel Hansen6.2k
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Comment: C: Removing GC content bias and trended bias from ChIP-seq data
... The issue we try to address with cqn is the fact that different samples can have very different GC bias. The bias does not cancel out if it is sample specific, and it is an observable fact that this could be the case. Having said that, it is entirely possibly to be lucky and analyze an experiment ...
written 3 months ago by Kasper Daniel Hansen6.2k

Latest awards to Kasper Daniel Hansen

Popular Question 16 months ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Appreciated 16 months ago, created a post with more than 5 votes. For Bioconductor on Coursera
Scholar 2.1 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.0 years ago, created 100 posts.

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