Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 686 results • page 1 of 69 • next >
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Answer: A: How to convert GenomicRatioSet to RGChannelSet in minfi::compartments()
... The output from estimateCellCounts is not corrected for cell type composition. The `normalizedData` returned by the function is probably not something you care about. It is your input data after being normalized together with the reference data. To correct for cell type composition you need to use ...
written 6 days ago by Kasper Daniel Hansen6.3k
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Comment: C: difference in detection p-values from Minfi vs. GenomeStudio
... Thats useful, esp. the expression link. Do you have a couple of IDAT files together with the output from GenomeStudio. I could implement their (weird) p-value calculation and we could check if we get the same as from GenomeStudio. You can share the stuff with me using for example Dropbox. Best, K ...
written 6 days ago by Kasper Daniel Hansen6.3k
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Comment: C: difference in detection p-values from Minfi vs. GenomeStudio
... The implementation in minfi is my interpretation of the only documentation I could find on what GenomeStudio actually does, which was a couple of sentences in the manual. If the manual has been expanded, or there is more information somewhere else, I am happy to take a look at it and consider chang ...
written 7 days ago by Kasper Daniel Hansen6.3k
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Answer: A: Meaning of the value column in bumphunter output (minfi package)
... That depends on your design matrix On Wed, May 17, 2017 at 10:28 AM, Antonio M. [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Antonio M. <https: support.bioconductor.org="" u="" 13072=""/> wrote Question: ...
written 7 days ago by Kasper Daniel Hansen6.3k
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Comment: C: "minfi" loading problem because of couldn't "bumphunter" load
... This is an rtracklayer issue. It appears to me that the shipped binaries (for rtracklayer) for OS X requires that libssl is installed. You should either install libssl, or (perhaps better) see if someone can fix the binaries. Best, Kasper On Sun, May 7, 2017 at 9:15 PM, gentryae [bioc] <norep ...
written 16 days ago by Kasper Daniel Hansen6.3k
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Comment: C: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... You probably do not want to use preprocessFunnorm with nPCs = 0. Best, Kasper On Tue, Apr 11, 2017 at 8:56 AM, rahel14350 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User rahel14350 <https: support.bioconductor. ...
written 6 weeks ago by Kasper Daniel Hansen6.3k
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Answer: A: how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
... It is not clear that combining two preprocessing methods is better than using either one of them individually. It is probably possible to hack the functions to do what you want, but it is not trivial, and it is not clear it is even a good idea. Best, Kasper On Wed, Apr 5, 2017 at 11:35 AM, rahel1 ...
written 7 weeks ago by Kasper Daniel Hansen6.3k
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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 11 weeks ago by Kasper Daniel Hansen6.3k
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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 11 weeks ago by Kasper Daniel Hansen6.3k
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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 12 weeks ago by Kasper Daniel Hansen6.3k

Latest awards to Kasper Daniel Hansen

Popular Question 13 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 13 months ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 13 months ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 13 months ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Appreciated 20 months ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 20 months ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 2.5 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.3 years ago, created 100 posts.

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