User: Hans-Ulrich Klein

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330
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Posts by Hans-Ulrich Klein

<prev • 32 results • page 1 of 4 • next >
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BiSeq - readBismark error
... 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 ...
biseq written 4.8 years ago by Hans-Ulrich Klein330 • updated 4.8 years ago by David Iles130
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Comment: C: setting names of GAlignmentsList objects
... 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 5.0 years ago by Hans-Ulrich Klein330
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setting names of GAlignmentsList objects
... 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 5.0 years ago by Hans-Ulrich Klein330 • updated 5.0 years ago by Martin Morgan ♦♦ 22k
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Bioinformatics Job at University of Münster
... 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 ...
sequencing written 5.5 years ago by Hans-Ulrich Klein330
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Maximal length of Rle vectors
... 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 ...
sequencing written 7.0 years ago by Hans-Ulrich Klein330 • updated 7.0 years ago by Hervé Pagès ♦♦ 13k
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Starr - MAT normalization
... 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 -- ...
normalization starr written 8.5 years ago by Hans-Ulrich Klein330 • updated 8.5 years ago by Raphael Gottardo40
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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 9.1 years ago by Hans-Ulrich Klein330
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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 9.1 years ago by Hans-Ulrich Klein330
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Ringo - finding enriched regions
... 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 ...
ringo written 9.1 years ago by Hans-Ulrich Klein330 • updated 9.1 years ago by Joern Toedling450
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Affymetrix Mouse Promoter array / pdInfoBuilder
... 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 ...
annotation oligo pdinfobuilder written 9.1 years ago by Hans-Ulrich Klein330 • updated 9.1 years ago by zacher@lmb.uni-muenchen.de50

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