User: Georg Otto

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Georg Otto120
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g**@well.ox.ac.uk

Posts by Georg Otto

<prev • 11 results • page 1 of 2 • next >
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overlap GRangesList and vcf
... Hi, I apologise if this is trivial, but I haven't found a straight forward way to do this so far. Given a GRangesList with exons ## exons by gene range.exon <- exonsBy(txdb.ensgene, "gene") and a vcf file with SNP data (positions, alleles, etc), how can I generate a list of exons that contai ...
snp written 6.8 years ago by Georg Otto120 • updated 6.8 years ago by Valerie Obenchain6.7k
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Answer: A: error in DEXSeq fitDispersionFunction()
... Thanks a lot! Now unfortunately I get a problem at the the size factor estimation step: > bat.counts <- estimateSizeFactors(bat.counts) Error in validObject(cds) : invalid class ?ExonCountSet? object: The featureNames do not match with the geneIDs:exonIDs Are there incompatibilities with th ...
written 6.8 years ago by Georg Otto120
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Answer: A: annotate htmlpage error
... "James W. MacDonald" writes: > Hi Martin, > > On 3/14/2012 4:36 PM, Martin Morgan wrote: >> On 03/14/2012 01:13 PM, Georg Otto wrote: >>> Hi, >>> >>> after updating the annotate package from 1.32.1 to 1.32.2 I get an error >>> using the htmlpage f ...
written 7.2 years ago by Georg Otto120
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annotate htmlpage error
... Hi, after updating the annotate package from 1.32.1 to 1.32.2 I get an error using the htmlpage function. Here with the old version: > htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus") &g ...
annotate written 7.2 years ago by Georg Otto120
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Answer: A: Problem installing GenomicFeatures
... Martin Morgan writes: > On 03/08/2012 10:01 AM, Georg Otto wrote: >> Martin Morgan writes: >> >>> On 03/08/2012 08:42 AM, Georg Otto wrote: >> Error : classes "file", "connection" are not exported by 'namespace:Biostrings' >> ERROR: lazy loading failed for pac ...
written 7.2 years ago by Georg Otto120
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Answer: A: Problem installing GenomicFeatures
... Martin Morgan writes: > On 03/08/2012 08:42 AM, Georg Otto wrote: >>> install.packages("GenomicFeatures", lib="/home/gwo/rlib") >> --- Please select a CRAN mirror for use in this session --- >> Loading Tcl/Tk interface ... done >> Warning message: >> In getDep ...
written 7.2 years ago by Georg Otto120
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Problem installing GenomicFeatures
... Dear Bioconductors, since my R installation was upgraded to 2.14.1 I have a problem with loading and installing GenomicFeatures. here is what I try to do: library(Biostrings) Loading required package: IRanges Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following ...
genomicfeatures written 7.2 years ago by Georg Otto120
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Answer: A: error in DEXSeq fitDispersionFunction()
... Wolfgang Huber writes: Dear Wolfgang, thanks for your help. I tried with version 1.1.1 and still got the same message: Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm, disps[good], start = coef ...
written 7.5 years ago by Georg Otto120
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error in DEXSeq fitDispersionFunction()
... Dear Bioconductors, I am trying to use DEXSeq to test for differential exon usage in my RNA-seq data. I was able to generate the exon count tables using the python scripts that come with the package and the function read.HTSeqCounts(). However, I get an error at this step: exon.counts <- fitDi ...
dexseq written 7.5 years ago by Georg Otto120
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Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
... Samantha England writes: > > I wrote for your advice last week concerning a problem I was experiencing using the "genes.rpt.agi" function in "Agi4x44PreProcess". > Here is the fault code, plus the traceback result: > >> genes.rpt.agi(dd, "zfcustomAG.db", raw.data = TRUE, WRITE.h ...
annotation probe written 8.8 years ago by Georg Otto120

Latest awards to Georg Otto

Popular Question 6.8 years ago, created a question with more than 1,000 views. For overlap GRangesList and vcf
Popular Question 6.8 years ago, created a question with more than 1,000 views. For Problem installing GenomicFeatures

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