Moderator: Kasper Daniel Hansen
Kasper Daniel Hansen ♦ 6.4k
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Posts by Kasper Daniel Hansen
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... Peter,
I took a more careful look at your report. Are the two different R installations (with and without OpenBLAS) compiled with different compilers? I know that Rgraphviz fails using GCC 8 with -O3 optimization flags, with this particular error (missing `***__pow_finite`). You don't mention in y ...
written 10 days ago by
Kasper Daniel Hansen ♦ 6.4k
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... First a clarification.
Version 2.26 is the Rgraphviz version
2.28 is the Graphviz versioon
they have nothing to do with each other, although now that 26 ~ 28 it looks
weird.
Second, I figured out what the issue is, but I dropped the ball in fixing
it.
On Wed, Nov 28, 2018 at 9:45 AM mmokrejs [ ...
written 11 days ago by
Kasper Daniel Hansen ♦ 6.4k
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... At first, I would use "standard" tools from GWAS to do this (not saying
this is easy), either on data in the unit interval or the logit
transformation. In principle all you need is a mixed effect model where the
covariance matrix reflects the relatedness structure.
On Sat, Aug 25, 2018 at 12:34 AM ...
written 3 months ago by
Kasper Daniel Hansen ♦ 6.4k
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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 3 months 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 months ago by
Kasper Daniel Hansen ♦ 6.4k
• updated 3 months ago by
shepherl ♦♦ 890
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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 4 months 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 5 months 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 7 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 9 months ago by
Kasper Daniel Hansen ♦ 6.4k
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177
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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 9 months ago by
Kasper Daniel Hansen ♦ 6.4k
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