User: Hans-Ulrich Klein
Hans-Ulrich Klein • 330
- Reputation:
- 330
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 4 years, 4 months ago
- Joined:
- 12 years, 1 month ago
- Email:
- h******@uni-muenster.de
Posts by Hans-Ulrich Klein
<prev
• 32 results •
page 1 of 4 •
next >
0
votes
1
answer
762
views
1
answer
... 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 5.0 years ago by
Hans-Ulrich Klein • 330
• updated
5.0 years ago by
David Iles • 130
0
votes
1
answer
516
views
1
answers
... 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 5.2 years ago by
Hans-Ulrich Klein • 330
0
votes
1
answer
516
views
1
answer
... 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 5.2 years ago by
Hans-Ulrich Klein • 330
• updated
5.2 years ago by
Martin Morgan ♦♦ 22k
0
votes
0
answers
395
views
0
answers
... 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 5.7 years ago by
Hans-Ulrich Klein • 330
0
votes
1
answer
533
views
1
answer
... 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 7.2 years ago by
Hans-Ulrich Klein • 330
• updated
7.2 years ago by
Hervé Pagès ♦♦ 13k
0
votes
1
answer
354
views
1
answer
... 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 8.7 years ago by
Hans-Ulrich Klein • 330
• updated
8.7 years ago by
Raphael Gottardo • 40
0
votes
1
answer
525
views
1
answers
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 9.3 years ago by
Hans-Ulrich Klein • 330
0
votes
1
answer
525
views
1
answers
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 9.3 years ago by
Hans-Ulrich Klein • 330
0
votes
1
answer
525
views
1
answer
... 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 9.3 years ago by
Hans-Ulrich Klein • 330
• updated
9.3 years ago by
Joern Toedling • 450
0
votes
2
answers
707
views
2
answers
... 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 9.3 years ago by
Hans-Ulrich Klein • 330
• updated
9.3 years ago by
zacher@lmb.uni-muenchen.de • 50
Latest awards to Hans-Ulrich Klein
Popular Question
4.3 years ago,
created a question with more than 1,000 views.
For Affymetrix Human Gene 1.0 ST Array
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 210 users visited in the last hour