User: Hans-Ulrich Klein
Hans-Ulrich Klein • 330
- Reputation:
- 330
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 5 years ago
- Joined:
- 12 years, 11 months ago
- Email:
- h******@uni-muenster.de
Posts by Hans-Ulrich Klein
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... Dear all,
We would like to inform users of the BiSeq package, that there was in
error in the readBismark() function that may - depending on the files
and the order they were read in - lead to false methylation values.
Affected BiSeq versions are 1.2.0 to 1.2.3. If you have used one of
these versio ...
written 5.7 years ago by
Hans-Ulrich Klein • 330
• updated
5.7 years ago by
David Iles • 130
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... Dear Martin,
yes, it is going nicely in the current release.
I pasted the sessionInfo() but did not look at it :/ Sorry.
Best,
Hans
On 31/10/13 12:45, Martin Morgan wrote:
> On 10/31/2013 02:53 AM, Hans-Ulrich Klein wrote:
>> Dear all,
>>
>> I can not change the list eleme ...
written 6.0 years ago by
Hans-Ulrich Klein • 330
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... Dear all,
I can not change the list element names of my GAlignmentsList objects:
library(GenomicRanges)
library(Rsamtools)
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
ga <- readGappedAlignments(ex1_file)
galist <- GAlignmentsList(one=gal, two=gal)
names(galist)
nam ...
written 6.0 years ago by
Hans-Ulrich Klein • 330
• updated
6.0 years ago by
Martin Morgan ♦♦ 23k
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... Dear List Members,
There is an open bioinformatics position for PhD candidates or post
docs
at the Univerity of M?nster (Institute for Medical Informatics). Focus
is on exome sequencing in a clinical environment. See the job
advertisement for more details:
http://klinikum.uni-muenster.de/index.php ...
written 6.4 years ago by
Hans-Ulrich Klein • 330
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... Dear all,
I observed this problem regarding the maximal length of a Rle vector:
> rle = Rle(rep(0, 1000000000))
> length(rle)
[1] 1000000000
> length(c(rle, rle, rle))
[1] -1294967296
Probably, it is caused by the maximum positive number (~2.1E9) that
can
be represented by an integer ...
written 7.9 years ago by
Hans-Ulrich Klein • 330
• updated
7.9 years ago by
Hervé Pagès ♦♦ 14k
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... Hi,
the Starr vignette on page 7 says: "Besides this normalization method,
there are e.g. median rank percentile , scale, quantile,
vsn, MAT and some others available." Which method provides MAT
normalization? "normalize.Probes()" does not according to its help
page.
Thanks you,
Hans-Ulrich
--
...
written 9.5 years ago by
Hans-Ulrich Klein • 330
• updated
9.5 years ago by
Raphael Gottardo • 40
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Comment:
C: Ringo - finding enriched regions
... Dear Joern,
your guess was right. It was an issue with my probeAnno object. I
created the probeAnno this way:
(reads is an AlignedRead object with all my probes)
pos = data.frame(CHROMOSOME=chromosome(reads),
PROBE_ID=as.character(id(reads)),
POSITION=position(rea ...
written 10.0 years ago by
Hans-Ulrich Klein • 330
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587
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Comment:
C: Ringo - finding enriched regions
... Dear Joern,
the feature names of my ExpressionSet instance are:
> all(featureNames(eSetS) == as.character(1:nrow(eSetS)))
[1] TRUE
So in my case both expressions
> exprs(eSetS)[as.numeric(chers[[1]]@probes),]
and
> exprs(eSetS)[chers[[1]]@probes,]
return the same probes that have log ...
written 10.0 years ago by
Hans-Ulrich Klein • 330
0
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1
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587
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... Hello,
I am confused about the results returned from the
"findChersOnSmoothed"
function in the Ringo package. I have an ExpressionSet object storing
normalized log ratios (ChIP / Control) from three replicates. I use
this
analysis workflow:
> eSetS = computeRunningMedians(eSet, probeAnno, modC ...
written 10.0 years ago by
Hans-Ulrich Klein • 330
• updated
10.0 years ago by
Joern Toedling • 450
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... Hi All,
I have ChIP-chip data based on the Affymetrix Mouse Promoter platform.
I
built a "pd.mm.prompr.v02" package with the pdInfoBuilder functions
and
read in the CEL files using the oligo package.
I get stuck with the genome coordinates of the probes provided by my
"pd.mm.prompr.v02" package. Th ...
written 10.0 years ago by
Hans-Ulrich Klein • 330
• updated
10.0 years ago by
zacher@lmb.uni-muenchen.de • 50
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