User: alessandro brozzi

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Posts by alessandro brozzi

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Comment: C: Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
... hi, I solved it setting no http proxy: Sys.setenv(http_proxy="") HTH alex     ...
written 2.9 years ago by alessandro brozzi120
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Answer: A: Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
... hi paul, > library(RCytoscape) Loading required package: graph Loading required package: XMLRPC > cw = new.CytoscapeWindow ("test", graph=RCytoscape::makeSimpleGraph ()) Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems > xml.rpc(cw@uri, "Cytoscape.test") Error in merge(list(...), ...
written 3.1 years ago by alessandro brozzi120
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Answer: A: Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
... hi Paul, fisrt of all thank you sincerely for the help you are providing. Here we go: > cw = new.CytoscapeWindow('vignette', graph=g, overwriteWindow=TRUE) Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems > traceback() 6: stop("Problems") 5: xml.rpc(obj@uri, "Cytoscape.version") 4: ...
written 3.1 years ago by alessandro brozzi120
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Answer: A: Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
... hi! Thank you very much for the suggestions. I made the R upgrade but the error is still there :( I don't really understand why from the console it perfectly works. May be due to some "proxy" configurations? BTW: Cytoscape rel: 2.8.3, plugin: 1.8 bests! Alex ...
written 3.1 years ago by alessandro brozzi120
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Answer: A: Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
... hi Andrzej, yes the session info are exactley the same. In th epast days did a lot of debugging. What I guess is something wrong here: > xml.rpc(cy.tmp,"Cytoscape.version") Error in .postForm(curl, .opts, .params, style) :   Unhandled case for the value of curl_easy_setopt (R type = 25, option ...
written 3.1 years ago by alessandro brozzi120
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Rcytoscape Rstudio Error in xml.rpc(obj@uri, "Cytoscape.version") : Problems
... Dears, I use Cytoscape 2.8 and Rcytoscape on my Ubuntu 64bit machine. If I start an R session from the terminal and I run the following code: library(RCytoscape) g = new("graphNEL", edgemode="directed") g = graph::addNode("U",g) cw = new.CytoscapeWindow("vignette" , graph=g, overwriteWindow=TRUE ...
rcytoscape xml software error written 3.1 years ago by alessandro brozzi120 • updated 3.0 years ago by drsuuzzz0
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Comment: C: HTqPCR: number of samples, number of features
... hi Heidi, with: n.data=40 n.features=96 it works fine. thank you very much! Alex On Mon, Sep 10, 2012 at 2:07 AM, Heidi Dvinge wrote: > Hi Alex, > > > hi, > > I've been given an SDS raw file (see below) which contains embedded 10 > > cards of 348 wells each. > > ...
written 5.2 years ago by alessandro brozzi120
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HTqPCR: number of samples, number of features
... hi, I've been given an SDS raw file (see below) which contains embedded 10 cards of 348 wells each. The genes are totally 48 and each card has 4 samples so totally 40 samples. If I am correct n.features should be = 3480 and the n.data (the number of samples that are present in each file) should be = ...
written 5.2 years ago by alessandro brozzi120 • updated 5.2 years ago by Heidi Dvinge2.0k
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Answer: A: IRanges problem: findOverlaps
... hi Nicolas, I don't know very well Iranges but to find overlapping intervals the package "intervals" http://cran.fhcrc.org/web/packages/intervals/index.html is very straightforward. Here an example: peaks = matrix( c( 2, 8, ...
written 5.4 years ago by alessandro brozzi120
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Answer: A: How do you find your orthologues?
... hi Karl, another possible solution might be the package "HomoVert": http://labs.fhcrc.org/fero/R/HomoVert.html that contains a Homologene (NCBI ) conversion table (currently Build 64) and functions that use this table to convert Entrez Gene IDs from one species to another. Alex On Tue, Jun 26, ...
written 5.4 years ago by alessandro brozzi120

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