Moderator: Kasper Daniel Hansen

Reputation:
6,280
Status:
Trusted
Location:
United States
Website:
http://www.hansenlab.org/
Twitter:
KasperDHansen
Scholar ID:
Google Scholar Page
Last seen:
1 month, 2 weeks ago
Joined:
12 years, 3 months ago
Email:
k*****************@gmail.com

Posts by Kasper Daniel Hansen

<prev • 700 results • page 2 of 70 • next >
0
votes
2
answers
182
views
2
answers
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 4 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
3.1k
views
1
answers
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 4 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
107
views
1
answers
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 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
189
views
1
answers
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 5 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
192
views
1
answers
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 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
291
views
1
answers
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 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
291
views
1
answers
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 6 months ago by Kasper Daniel Hansen6.3k
0
votes
1
answers
250
views
1
answers
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 6 months ago by Kasper Daniel Hansen6.3k
0
votes
4
answers
468
views
4
answers
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 6 months ago by Kasper Daniel Hansen6.3k
0
votes
3
answers
371
views
3
answers
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 7 months ago by Kasper Daniel Hansen6.3k

Latest awards to Kasper Daniel Hansen

Popular Question 19 months ago, created a question with more than 1,000 views. For support for EPIC methylation arrays in minfi
Scholar 19 months ago, created an answer that has been accepted. For A: Minfi User Guide Build Problem?
Scholar 19 months ago, created an answer that has been accepted. For A: Minfi RGChannelSet preprocessing error in assayDataElement
Scholar 19 months ago, created an answer that has been accepted. For A: Covert MethylSet to RGChannelSet object
Appreciated 2.2 years ago, created a post with more than 5 votes. For Bioconductor on Coursera
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Bioconductor on Coursera
Scholar 3.0 years ago, created an answer that has been accepted. For A: QC/normalization standards for cancer studies with 450k array data
Centurion 7.8 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 179 users visited in the last hour