User: Yan Jiao

gravatar for Yan Jiao
Yan Jiao140
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8 years, 2 months ago
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8 years, 11 months ago
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y*****@ucl.ac.uk

Posts by Yan Jiao

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Biomart with human genes NCBI 35/hg17
... Hi Steffen, I also tried using lift genome annotations for mapping different built: http://genome.ucsc.edu/cgi-bin/hgLiftOver It helps a bit, but some regions it couldn't give me the mapping result, e.g. Failed input regions: #Split in new chr1:0-245500000 #Partially deleted in new ...
written 8.2 years ago by Yan Jiao140
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Biomart with human genes NCBI 35/hg17
... Dear All, I'm trying to use the previous built (within Biomart)for human genes to get gene location, It seems like Ensembl 44 is the version I should use for NCBI 35/hg17, I did following: ensembl =useMart("ensembl_mart_44",archive=TRUE) listDatasets(ensembl) [1] dataset description version & ...
written 8.2 years ago by Yan Jiao140 • updated 8.2 years ago by Steffen Durinck540
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DNAcopy
... Dear all I'm using DNAcopy package to do copynumber segmentation, I'm just wondering how to output the result to a file? the class of the object is DNAcopy, I could use print() to see it on the screen , i want to either change the result into a matrix format or write it directly to a .txt file or . ...
dnacopy copynumber written 8.4 years ago by Yan Jiao140 • updated 8.4 years ago by Sean Davis21k
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Comment: C: CGHcall
... Thanks Achilleas, But what if the data I got is segmented already, how could I skip segmentation step and using CGHcall directly? Many thanks Yan From: Achilleas Pitsillides [mailto:anp4r@virginia.edu] Sent: 26 May 2011 18:57 To: Yan Jiao; bioconductor@r-project.org Subject: Re: [BioC] CGHcall ...
written 8.4 years ago by Yan Jiao140
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CGHcall
... Dear All, I'm trying to run the examples given by CGHcall manual: # create an instance of cghCall new("cghCall") # create an instance of cghCall through \code{\link{ExpandCGHcall}} ## Not run: data(Wilting) rawcgh <- make_cghSeg(Wilting) normalized <- normalize(rawcgh) but I got error: cou ...
cghcall written 8.4 years ago by Yan Jiao140 • updated 8.4 years ago by Sean Davis21k
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how to map choromosome location to gene ID
... Dear all, I'm trying to use biomaRt to map the chromosome location to gene ID,( I got chromosome number, start position and stop position, and it's for human) May I ask the syntax of it? Many thanks YAn [[alternative HTML version deleted]] ...
biomart written 8.4 years ago by Yan Jiao140 • updated 8.4 years ago by Steffen Durinck540
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Comment: C: KEGGgraph help
... No, it crashed From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: 29 November 2010 16:48 To: Yan Jiao Cc: bioconductor@r-project.org Subject: Re: [BioC] KEGGgraph help Hi dear Yan, Maybe give a try to draw a toy network V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, ...
written 8.9 years ago by Yan Jiao140
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Comment: C: KEGGgraph help
... sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached b ...
written 8.9 years ago by Yan Jiao140
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KEGGgraph help
... Dear all, I managed reading in a kegg graph A graphNEL graph with directed edges Number of Nodes = 70 Number of Edges = 109 but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can I see the graph? Many thanks yan ************************************************* ...
graph written 8.9 years ago by Yan Jiao140 • updated 8.9 years ago by Jitao David Zhang340
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Comment: C: (no subject)
... Thanks david, One stupid question, I couldn't find hsa05211 on the KEGG server. Where to download? Many thanks yan From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: 29 November 2010 12:42 To: Yan Jiao Cc: bioconductor@r-project.org Subject: Re: [BioC] (no subject) Hi de ...
written 8.9 years ago by Yan Jiao140

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Popular Question 8.2 years ago, created a question with more than 1,000 views. For how to map choromosome location to gene ID

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