User: Tony Chiang

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Tony Chiang570
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Posts by Tony Chiang

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Comment: C: Question about package "RpsiXML", URL as input for parsePsimi25Interaction()
... I don't think that it is a question of parsing perse. Here is what I would do: Obtain the XML file(s) you would like; that is the XML files pertaining your organism of interest. Parse the entire file and get the all the interactions contained in those files. RpsiXML should build you a graph (or gra ...
written 8.9 years ago by Tony Chiang570
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Comment: C: load failed for 'Rlibstree'
... Hi Paul, 2010/4/8 Paul Shannon > Herve & Seth, > > Thanks for your replies. Yes, it must be the snow leopard binary problem. > > I've tried biocLite (c ('microRNA', 'Rlibstree')) a few times, always with > the same problem. > > I should know this, but don't: what's ...
written 9.7 years ago by Tony Chiang570
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Comment: C: Search queries with biomaRt does not align with online queries via ensembl
... Hi James, See inline... On Mon, Mar 1, 2010 at 7:55 AM, James W. MacDonald wrote: > Hi Tony, > > ATF4 isn't a valid gene name, it's a HUGO gene symbol. The gene name can be > retrieved using the 'description' attribute. So you have to know that ATF4 > is a gene symbol, and that Ens ...
written 9.8 years ago by Tony Chiang570
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Comment: C: Search queries with biomaRt does not align with online queries via ensembl
... Hi Hans, Yes that was all very helpful. So my mistake was to assume that a gene name is the actual name of the gene rather than a description of the gene. It is there in the documentation so I should not complain...though very counter-intuitive I would argue. Thanks for all your help on this! Che ...
written 9.8 years ago by Tony Chiang570
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Answer: A: Search queries with biomaRt does not align with online queries via ensembl
... Thanks Hans, That worked much better. Quick follow up question then (I guess for anyone who might know the answer), when would we use the hgnc gene names rather the the symbols? It would appear that ATF4 is a valid hgnc gene name so I thought that the obvious choice would have been to filter based ...
written 9.8 years ago by Tony Chiang570
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Search queries with biomaRt does not align with online queries via ensembl
... Hi Steffen et al, Quick question about a search query via biomaRt. Here is the code that I am using: ***** library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") filters = listFilters(ensembl) attributes = listAttributes(ensembl) getBM(attributes=c("ensembl_peptide_id", " ...
go hgu133plus2 biomart written 9.8 years ago by Tony Chiang570
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[Bioc-devel] BSgenome error
... Hi Julie, Let's keep this on the list. First off, you should only send issues to bioc-devel when you are using the devel version of R and Bioc. It seems like you are using the current release version of R and Bioc so you should really send these messages to the Bioc list (which I have copied here a ...
go bsgenome iranges chippeakanno written 10.0 years ago by Tony Chiang570
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Answer: A: RpsiXML issues with latest Biogrid release files
... Hi Sara, The current release of R is 2.10. I don't know if this will fix the problem, but the current versions of the packages are built for the latest release of R, so the first thing to try is updating your R which will update the version of RpsiXML. I will look at your example in a bit. Tony O ...
written 10.0 years ago by Tony Chiang570
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translateID in RpsiXML: [was] problems getting new intact networks from ppiDatwa
... So the documentation is off. I have copied the package maintainer to this e-mail thread so that he might be able to fix the man pages. Quick answer to the supported IDs. The translateID method basically tries to work with the repositories. If a particular repository has annotated UniprotKB, Gene Na ...
biomart written 10.0 years ago by Tony Chiang570
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Answer: A: problems getting new intact networks from ppiData
... Hi Sara, A big mea culpa on my part here. I meant to deprecate the ppiData package as it is no longer necessary. When I first started this work, I had some ad hoc functions to parse the IntAct repository. There is now the RpsiXML package where the user can parse the XML data files to get the latest ...
written 10.0 years ago by Tony Chiang570

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