User: Simon Anders

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Simon Anders150
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Posts by Simon Anders

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Comment: C: variation between cells compared to samples
... Hi Pete On Wed, 24 Feb 2010 07:19:55 -0800, Pete Shepard wrote: > The distance matrix works nicely however, I am having trouble plotting the > two scv curves to one panel, any suggestions. I can give to cds "cds <- > newCountDataSet( countsTable, conds )" a set of count data based on o ...
written 9.7 years ago by Simon Anders150
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Error in AnnotationDbi 1.7.8
... Hi I've just tried to update my Bioc 2.5 installation (on Ubuntu Intrepid x86_64) to the current packages, and AnnotationDbi 1.7.8 fails to install: ---8<--- * installing *source* package ?AnnotationDbi? ... [...] Creating a new generic function for "mget" in "AnnotationDbi" Creating a new gene ...
annotationdbi written 10.2 years ago by Simon Anders150 • updated 10.2 years ago by Tony Chiang570
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Answer: A: R: is there an identifier that uniquely identifies a gene all over the many data
... Hi mauede at alice.it wrote: > I forgot to specify that I am only dealing with Human species. > I used the ENSGxxxxx identifier to get out some data that I hoped would > uniquely identify the gene. > > > gene.map <- > getBM(attributes=c("hgnc_symbol","external_gene_id","re ...
written 10.3 years ago by Simon Anders150
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Answer: A: is there an identifier that uniquely identifies a gene all over the many databas
... Hi Maura mauede at alice.it wrote: > By trial-and-error it seems the attribute "hgnc_symbol" yields a unique gene identifier ... but I am not quite sure. > Instead a variable numbers of " refseq_dna" values are listed for the same "hgnc_symbol". HGNC is the Human Genome Organisation's Gene N ...
written 10.3 years ago by Simon Anders150
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biomaRt does not like flies
... Hi, I'm trying to access Ensembl's D. melanogaster dataset via biomaRt. This here works fine: mart <- useMart( "ensembl", dataset="hsapiens_gene_ensembl" ) This command here, however, causes the R process to hang: mart <- useMart( "ensembl", dataset="dmelanogaster_gene_ensembl" ) If I us ...
process biomart written 10.3 years ago by Simon Anders150
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Bug in GenomeGraphs: makeGeneRegion fails on regions devoid of genes
... Hi Steffen I've just found a bug in GenomeGraphs. Try this code: library(GenomeGraphs) mart <- useMart("ensembl", dataset = "mmusculus_gene_ensembl") start <- 51000000 end <- 51100000 plusStrand <- makeGeneRegion( chromosome = 10, start = start, end = end, str ...
biomart genomegraphs written 10.4 years ago by Simon Anders150
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interoperability between IRanges/ShortRead and rtracklayer
... Dear Patrick, Herv?, Michael or Martin I'm unclear on how to get from an IRanges Rle object to a RangedData object to use with rtracklayer's export function. The use case is as follows: Let's say I caclulate a coverage vector from some ChIP-Seq data, e.g.: library(IRanges) library(ShortR ...
coverage rtracklayer iranges written 10.4 years ago by Simon Anders150 • updated 10.4 years ago by Patrick Aboyoun1.6k
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rtracklayer: Problems running vignette
... Hi Michael, I've just tried to use rtracklayer, following your vignette, and ran into two problems. 1. I cannot add any tracks to a session. I entered the code in the vignette to produce the "targets" track and exported it as "targets.bed". To make things easier to follow, let's say, I start fro ...
rtracklayer written 10.4 years ago by Simon Anders150 • updated 10.4 years ago by Michael Lawrence620
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Answer: A: past bioc releases
... Hi, wangchuanming wrote: > On a Windows XP (SP2) machine, when I use the package Affy (R 2.0.1, > bioconductor 1.6),the following error message appears: > > >> library(affy) Data <- ReadAffy() eset <- rma(Data) > Error in load(zfile, envir = envir) : ReadItem: unknown typ ...
written 10.4 years ago by Simon Anders150
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Answer: A: HilbertVis troubles
... Hi Tobia, Tobias Straub wrote: > i want to visualize my tiling array data with HilbertVis and failed > using the hilbertImage function. > I get a proper plot using plotLongVector but when i call the > hilbertImage function i get "Error: length(vec) >= newLength is not TRUE". > all ...
written 10.4 years ago by Simon Anders150

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