Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.4k
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Posts by Kasper Daniel Hansen
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Comment:
C: annotationhub: data update
... In this case, this is an interface to a UCSC resource which I believe is
provided by the core team (I could be wrong though).
The implications (to me) is that as time goes on, the AnnotationHub version
of the resource deviates from UCSC. I understand short term deviations in
the sense that UCSC ha ...
written 2 days ago by
Kasper Daniel Hansen ♦ 6.4k
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... If I run the following code to get RefSeq from UCSC:
library(AnnotationHub)
ahub <- AnnotationHub()
ahub <- subset(ahub, species == "Homo sapiens" & genome == "hg19")
query(ahub, "refseq")[1]
I see
> query(ahub, "refseq")[1]
AnnotationHub with 1 record
# snapshotDate(): 2018-08-01 ...
written 3 days ago by
Kasper Daniel Hansen ♦ 6.4k
• updated 2 days ago by
shepherl ♦♦ 650
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... Its a tough one. From the density plot it is a bit of an outlier which is
never a good sign. On the other hand, the density per se does not look
horrible. I would say it requires more information
On Wed, Jul 25, 2018 at 10:54 PM peter.fransquet [bioc] <
noreply@bioconductor.org> wrote:
> ...
written 23 days ago by
Kasper Daniel Hansen ♦ 6.4k
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... This could well be a bug.
Does it work if you just run your data through preprocessQuantile?
Best,
Kasper
On Wed, Jun 20, 2018 at 3:13 PM, fgc [bioc] <noreply@bioconductor.org>
wrote:
> Activity on a post you are following on support.bioconductor.org
>
> User fgc <https: suppor ...
written 8 weeks ago by
Kasper Daniel Hansen ♦ 6.4k
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... You have set up your R installation to use MKL, but you have not done it
correctly. You need to sort this out with a sysadmin. You could benefit
from consulting the R installation manual. This is something you need to
fix at the R installation level (I think, unless you have local overrides).
Kas ...
written 3 months ago by
Kasper Daniel Hansen ♦ 6.4k
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Comment:
C: Libgomp error in IHW
... We have been using the package successfully quite a few times, so I don't think it is a basic issue. It could depend on this exact set of p-values. I think we have a LOT of p-values for this application, but I will let Kipper speak to the details here.
...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.4k
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Comment:
C: cpgCollapse in Minfi
... Thanks for answering this. Two points
1) The point of cpgCollapse is essentially to group CpGs into units. By
design each unit may contain >1 CpG so its not really possible to use the
name.
2) The name cgXXXXX is in fact informative. According to Illumina, the
XXXXX is a hash of the local seq ...
written 5 months ago by
Kasper Daniel Hansen ♦ 6.4k
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... Have you checked whether your system is current by running
biocValid()
...
written 6 months ago by
Kasper Daniel Hansen ♦ 6.4k
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717
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Comment:
C: Rgraphviz installation fails
... I have a hard time fully understanding your message, but it seems to me
that you're saying everything works now?
Best,
Kasper
On Wed, Jan 10, 2018 at 7:05 AM, Giovanni Calice [bioc] <
noreply@bioconductor.org> wrote:
> Activity on a post you are following on support.bioconductor.org
> ...
written 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
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... The number of probes inside an IDAT file depends on the settings of the
scanner at the time of the scanning of the file. This is encaptured in a
so-called DMAP file. Unfortunately, Illumina has releaed multiple DMAP
files for the EPIC chip so it is quite standard to see what you see. This
was never ...
written 7 months ago by
Kasper Daniel Hansen ♦ 6.4k
Latest awards to Kasper Daniel Hansen
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