Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 679 results • page 1 of 68 • next >
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Comment: C: minfi "mapToGenome" dimension error
... You have multiple packages which are out of date and which minfi depends on. Update and try again. The output of biocValid() should preferably be TRUE. What is the output of ncol(ratioset_raw)? 1? On Wed, Mar 8, 2017 at 1:58 PM, nhejazi [bioc] <noreply@bioconductor.org> wrote: > Activi ...
written 22 days ago by Kasper Daniel Hansen6.2k
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Answer: A: minfi "mapToGenome" dimension error
... Could you run your code and then immediately when you get an error do traceback() Also give us output of sessionInfo() biocValid() The last might require that you source biocLite Best, Kasper (Sent from my phone.) > On Mar 8, 2017, at 03:17, nhejazi [bioc] <noreply@bioconductor.org&g ...
written 22 days ago by Kasper Daniel Hansen6.2k
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Answer: A: warning message with BSseq function
... You give it vectors of (chr, pos). These have duplicates. Say for example chr1, 888 appears twice. Then we sum up the Cov and M matrices over those two entries. Best, Kasper On Mon, Feb 27, 2017 at 8:46 AM, marie.trijau [bioc] < noreply@bioconductor.org> wrote: > Activity on a post ...
written 4 weeks ago by Kasper Daniel Hansen6.2k
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Answer: A: minfi and lumi not available for version 3.3.2
... Use biocLite() Best, Kasper (Sent from my phone.) ...
written 4 weeks ago by Kasper Daniel Hansen6.2k • updated 4 weeks ago by Martin Morgan ♦♦ 19k
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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 5 weeks 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 10 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 11 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 11 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 3 months 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 3 months ago by Kasper Daniel Hansen6.2k

Latest awards to Kasper Daniel Hansen

Popular Question 11 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 11 months ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 11 months ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 11 months ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Appreciated 18 months ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 18 months ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 2.3 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.2 years ago, created 100 posts.

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