User: Steffen

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Steffen500
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Posts by Steffen

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Comment: C: biomaRt - batch query for chromosome location to gene identifier?
... Hi Kemal, The combo filter chromosome_name, start and end position is interpreted by the Ensembl BioMart as 'give everything on this chromosome between the given start and end position'. However this combo filter is an exception to other filters, that it doesn't know what to do when you give it a ...
written 7.9 years ago by Steffen500
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Answer: A: biomaRt query : inconsistent results for different Attribute set
... Dear Mamun, Thank you for reporting this inconsistent behavior. It looks like a bug at the http://www.biomart.org side not the biomaRt package. I'll contact the developers to see what is going on. Cheers, Steffen On Thu, Oct 21, 2010 at 6:57 AM, Md.Mamunur Rashid wrote: > Dear List, > I a ...
written 8.0 years ago by Steffen500
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Answer: A: omitted rows using getBM
... Hi Wyatt, Ensembl does it's own mapping of affy ids to the genome. If they decide there is no good match for an affy probe to the genome then they won't provide any result for that probe, which explains the reduced number of rows. Cheers, Steffen On Wed, Oct 13, 2010 at 2:32 PM, Mcmahon, Kwyatt ...
written 8.0 years ago by Steffen500
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Comment: C: mouse SNPs
... Hi Galina, Those are Ensembl exon identifiers. Unfortunately there is no exon idenfier filter in the Ensembl mouse BioMart so you cannot use an exon identifier directly as input for a getBM query. You could however get an exon to gene id mapping as follows: mouse=useMart("ensembl",dataset="mmuscu ...
written 8.1 years ago by Steffen500
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Answer: A: E. coli annotation to map?
... Hi Rayna, Did you check the bacteria ensembl BioMart? If you do: > library(biomaRt) > listMarts() biomart 1 ensembl 2 snp 3 functional_genomics 4 vega 5 bacterial_mart_5 The 5th biomart is ...
written 8.2 years ago by Steffen500
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Answer: A: biomaRt and hapmap "virtualSchema" parameter mis-specification
... Hi Andrew, Which version of biomaRt are you using? This should be fixed in the devel version of biomaRt which you can download from here: http://www.bioconductor.org/packages/devel/bioc/html/biomaRt.html Let me know if this doesn't work. Cheers, Steffen On Fri, Aug 20, 2010 at 12:46 PM, Andrew ...
written 8.2 years ago by Steffen500
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Answer: A: Limit for chromosomal regions in biomaRt?
... Hi Christian, Technically there is no limit. But for queries where I expect a lot of data to be returned, I usually split the query in a few smaller ones. However, for your query I would not expect that huge amount of data to be returned. This is not a biomaRt issue but an Ensembl issue and you mig ...
written 8.2 years ago by Steffen500
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Answer: A: biomaRt bug - shuffling getBM headers and content
... Hi Nenad, Thanks for reporting this. I'll look into what is causing this. Most likely it is a bug at the Ensembl BioMart server side and not the biomaRt package. Cheers, Steffen On Thu, Jul 8, 2010 at 9:24 AM, Nenad Bartonicek wrote: > Hi, > > I would like to report a bug in biomaRt ...
written 8.3 years ago by Steffen500
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Answer: A: error/problem with biomaRt gene symbol query
... HI Sergii, biomaRt will only return a result when there is a mapping for a probe to a gene. Can you do: genes=getBM(attributes = c("hgnc_symbol","ensembl_gene_id","chromosome_name","start_position"," end_position") , mart = ensembl) And then loop over this result to map your probes to genes? (an ...
written 8.3 years ago by Steffen500
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Answer: A: biomaRt: error using dataset from HapMap_rel27 mart
... Hi Brad, I recently fixed this and it should work using the devel version of biomaRt which you can get from here: http://www.bioconductor.org/packages/2.7/bioc/html/biomaRt.html Using that version I get the following: > hapmap<-useMart("HapMap_rel27") > hapmap<-useDataset("hm27_varia ...
written 8.3 years ago by Steffen500

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