Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.3k
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Posts by Kasper Daniel Hansen
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
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... 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 Hansen ♦ 6.3k
0
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... 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 Hansen ♦ 6.3k
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151
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... 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 Hansen ♦ 6.3k
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
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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