Moderator: Kasper Daniel Hansen

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Posts by Kasper Daniel Hansen

<prev • 692 results • page 1 of 70 • next >
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Answer: A: minfi - error when reading idat files
... This looks good to me. You don't get an error with force=TRUE. What you're seeing is that you have two sets of IDAT files scanned with different scan settings (specifically with different DMAP files). We see this a lot with the EPIC array. It is unfortunate that Illumina has released some many D ...
written 22 days ago by Kasper Daniel Hansen6.3k
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Comment: C: support for EPIC methylation arrays in minfi
... The latest stable version is 1.22.1. You should update R and Bioconductor. On Fri, Jun 30, 2017 at 3:55 AM, r.clifford [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User r.clifford <https: support.bioconductor.org ...
written 27 days ago by Kasper Daniel Hansen6.3k
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Answer: A: Unusually long running times for getMeth function since latest release
... This should not happen, but clearly it does. We could use (a lot) more information about what is going on, including the length of the BSseq object and the ranges. Could you perhaps post this as an issue on our Github page. What is the backend of the BSseq object? Best, Kasper On Thu, Jun 29, 20 ...
written 28 days ago by Kasper Daniel Hansen6.3k
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Comment: C: support for EPIC methylation arrays in minfi
... Yes it is. What version of minfi are you using? Best, Kasper On Thu, Jun 29, 2017 at 5:23 AM, r.clifford [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User r.clifford <https: support.bioconductor.org="" u="" 12781 ...
written 28 days ago by Kasper Daniel Hansen6.3k
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Answer: A: FuntooNorm on 450K and Epic data combined RGSet
... The authors of funtooNorm should modify their code to work with subsetted objects. This is something we now fully support in minfi and they can look in minfi to see examples of how to write it. One advantage of working with subsetted objects is to allow things like this. Best, Kasper On Tue, Jun ...
written 5 weeks ago by Kasper Daniel Hansen6.3k
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Comment: C: bsseq combineList: how to get an HDF5Array-backed object as return value?
... We should make this (and other) function(s) auto-guess the backend of the output. Obv. the default when input is all HDF5 should be HDF5 and likewise if all input is in-memory matrices. Should have capability of overriding of course. On Sat, Jun 10, 2017 at 1:20 AM, Martin Aryee [bioc] < norepl ...
written 6 weeks ago by Kasper Daniel Hansen6.3k
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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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by Kasper Daniel Hansen6.3k

Latest awards to Kasper Daniel Hansen

Popular Question 15 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 15 months ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 15 months ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 15 months ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Appreciated 22 months ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 22 months ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 2.6 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.5 years ago, created 100 posts.

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