User: steffen@stat.Berkeley.EDU

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Posts by steffen@stat.Berkeley.EDU

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Answer: A: getBM
... Dear Andreia, The result of a biomaRt query is indeed not sorted according to the input. There is not a one to one mapping for all three identifiers you are querying for. This partially explains the expansion in your result. In addition, Ensembl annotates everything to the transcript and some tran ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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unexpected genes names list using getBM{biomaRt}
... Hi Ramzi, When using multiple filters with more than one value for each filter, the BioMart webservice won't match up the different values for each filter. For example the following query: getBM(c("hgnc_symbol","chromosome_name","start_position","end_position "),filters=c("chromosome_name","start ...
alignment convert biomart written 8.0 years ago by steffen@stat.Berkeley.EDU600
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Answer: A: getBM function in biomaRt
... Hi Tim, biomaRt works with archives from about Ensembl version 52 and upwards. Hg17 corresponds to NCBI35 which is in Ensembl 35, you'll need to get a very old archive. You could get the data you need via the web BioMart interface: http://nov2005.archive.ensembl.org/index.html follow the BioMart ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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Answer: A: R: R: BioMart error occurred again
... Hi Maura, With "query in batch" I meant querying multiple IDs at once, not one at a time. There should be a way to convert your query from querying every id one by one to a query for everything in batch and then combine the results in R. For example: 1) you make a vector with all the target tran ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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Comment: C: BiomaRt return value
... Hi Tony, I want to add that in the past we used to return what was used as input to the query (filter) also as an attribute. However this is not generalizable as for some attributes/filters the name is different e.g. "start_position" in attribute list and "start" in filter list. And sometimes a f ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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Answer: A: BioMart error
... Hi, Would it be possible to include the query you were attempting that generated this error? Steffen > > OPEN NEW CONNECTION ON FILE: hsa-miR-31_V_MirBase_FastaFiles.txt > > **** WRITE 3UTR SEQUENCE TO FILE: hsa-miR- 31_V_MirBase_FastaFiles.txt > **** > > Error in getBM ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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Comment: C: Error using makeGeneRegion/getBM/listFilters, argument 'what' contains an invali
... Hi Tejal, You'll need to do your query using the web interface at: http://aug2007.archive.ensembl.org/biomart/martview/ export as a tab delimited file and import that in R. Cheers, Steffen > Hi Steffen, > You are right, this version is too old, but I need to use the older > version. &g ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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Answer: A: Error using makeGeneRegion/getBM/listFilters, argument 'what' contains an invali
... Hi Tejal, Ensembl 46 is to old and there have been some major changes since for biomaRt to work with it. Would a more recent ensembl archive work for you? For example Ensembl 54 is NCBI36 and might be what you were looking for unless you have another reason to specifically want Ensembl 46? You can ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600
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biomaRt- incorrect number of transcripts
... Dear Robert, Would it be possible to check if there are duplicates in the result you obtain via the web? By default biomaRt will retrieve only unique results, sometimes when you query over the web results are duplicated. To remove these you need to check the unique only checkbox when exporting yo ...
biomart written 8.0 years ago by steffen@stat.Berkeley.EDU600 • updated 8.0 years ago by Rhoda Kinsella660
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Answer: A: biomaRt * search
... Hi Paul, The * symbol is not usable in your biomaRt query. But you could do the following: library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") hgnc=getBM(attributes = c("hgnc_symbol", "ensembl_gene_id"), filters="with_hgnc", values=TRUE,mart=ensembl) hgnc[grep("PDE", ...
written 8.0 years ago by steffen@stat.Berkeley.EDU600

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