User: Hans-Ulrich Klein

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Posts by Hans-Ulrich Klein

<prev • 32 results • page 2 of 4 • next >
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GSEABase GOCollection wrong ontology
... Dear All, I want to generate sets of probes from the affy hgu133plus2 chip from the GO "Molecular Function". I used the GSEABase package: > library("GSEABase") > sets = GeneSetCollection(idType=AnnotationIdentifier("hgu133plus2.db"), setType=GOCollection(ontology="MF")) > sets[[1]] set ...
annotation go hgu133plus2 affy gseabase written 10.7 years ago by Hans-Ulrich Klein330 • updated 10.7 years ago by Martin Morgan ♦♦ 24k
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Answer: A: Error in assign while calling the vmatchPattern function
... Hi all, I encountered a similar (probably related) error today. I wanted to match a few hundred sequences against the UCSC genome from the package "BSgenome.Hsapiens.UCSC.hg18". I implemented a simple "for" loop and called seq = DNAString(sequences$Sequence[i]) matchRes = matchPattern(seq, ...
written 10.7 years ago by Hans-Ulrich Klein330
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limma - different parametrization and weights
... Dear All, I used limma with two different parametrizations. Both approaches should be equivalent in my opinion. However, if I use weights, the results differ. (Results of both approaches are equal without weights.) I attached an example below. Does someone know the reason for this? Regards, Hans-U ...
limma written 11.0 years ago by Hans-Ulrich Klein330
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Answer: A: Affymetrix Human Gene 1.0 ST Array
... Dear Benilton, thanks for your reponse. I built a pdInfoPackage as suggested: library(pdInfoBuilder) pgfFile = "HuGene-1_0-st-v1.r3.pgf" clfFile = "HuGene-1_0-st-v1.r3.clf" probeFile = "HuGene-1_0-st-v1.probe.tab" transFile = "HuGene-1_0-st-v1.na24.hg18.transcript.csv" pkg <- new("AffyGenePDIn ...
written 11.5 years ago by Hans-Ulrich Klein330
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Affymetrix Human Gene 1.0 ST Array
... Dear List, I would like to analyze Hume Gene 1.0 ST Arrays using BioC. I am interested in differential expression at probeset and at gene level. Searching the list archives reveals, that "makecdfenv and makePlatformDesign make the assumption that there is a one-to-one mapping of probe ==> probes ...
infrastructure cdf probe affy written 11.5 years ago by Hans-Ulrich Klein330
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Comment: C: matching transcription factor binding sites
... Hi Herve, Herve Pages wrote: > Hans-Ulrich Klein wrote: >> I want to locate transcription factor binding sites (tfbs) within a >> given sequence. The tfbs are derived from databases like transfac or >> jaspar and are described by matrices. Are there algorithms for >> loca ...
written 11.6 years ago by Hans-Ulrich Klein330
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matching transcription factor binding sites
... Dear all, I want to locate transcription factor binding sites (tfbs) within a given sequence. The tfbs are derived from databases like transfac or jaspar and are described by matrices. Are there algorithms for locating tfbs matches (e.g. "matinspector") implemented in bioconductor? I could not find ...
transcription written 11.6 years ago by Hans-Ulrich Klein330 • updated 11.6 years ago by Hervé Pagès ♦♦ 14k
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GSEABase - mapIdentifiers
... Hello all, the function mapIdentifiers() works fine for "GeneSet" objects whereas it throws an error message when a "GeneColorSet" is given: > library("GSEABase") > gs = GeneColorSet(geneIds=c("TYMP", "XPO1", "LBR"), geneIdType=SymbolIdentifier(), setName="t ...
written 11.7 years ago by Hans-Ulrich Klein330 • updated 11.7 years ago by Martin Morgan ♦♦ 24k
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Comment: C: limma with missing values
... Dear Gordon, thank you very much for your reply! Gordon K Smyth wrote: > The output that you give does not match your code.[...] I am sorry for that. I wrote conts = list(treat="contr.sum", class="contr.treatment") in my posting but actually used conts = list(treat="contr.treatment", class="co ...
written 11.7 years ago by Hans-Ulrich Klein330
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limma with missing values
... Dear all, I am struggling with using limma in the case of many missing values. Here is a small example: df = data.frame( g1=c(5,5,6,6,NA,NA), g2=c(5,5,NA,NA,6,6), g3=c(NA,NA,5,5,6,6), treat=c("T1","T1","T2","T2","T3","T3"), class=c("A","B","A","B","A","B")) conts = list(treat="contr.s ...
limma written 11.7 years ago by Hans-Ulrich Klein330 • updated 11.7 years ago by Gordon Smyth39k

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Popular Question 5.2 years ago, created a question with more than 1,000 views. For Affymetrix Human Gene 1.0 ST Array

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