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@w-evan-johnson-5447
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array chip ▴ 360
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Hi, I was trying to use cytoscapePlot() from the graphite package, but got the error message below: > library(graphite) > cytoscapePlot(convertIdentifiers(reactome$Unwinding of DNA, "symbol")) Loading required package: RCytoscape Loading required package: XMLRPC Error in function (type, msg, asError = TRUE)Â : couldn't connect to host In addition: Warning messages: 1: package âRCytoscapeâ was built under R version 2.15.2 2: package âXMLRPCâ was built under R version 2.15.2 What's the problem here? thanks! John [[alternative HTML version deleted]] ADD COMMENT 0 Entering edit mode Hi John, This usually means that Cytoscape is not running, or that the CytoscapeRPC plugin is not enabled, or not enabled on the correct port. Let us know if you still have trouble after these things are set up. - Paul On Jan 21, 2013, at 2:58 PM, array chip wrote: > Hi, I was trying to use cytoscapePlot() from the graphite package, but got the error message below: > >> library(graphite) >> cytoscapePlot(convertIdentifiers(reactome$Unwinding of DNA, "symbol")) > Loading required package: RCytoscape > Loading required package: XMLRPC > Error in function (type, msg, asError = TRUE) : couldn't connect to host > In addition: Warning messages: > 1: package ?RCytoscape? was built under R version 2.15.2 > 2: package ?XMLRPC? was built under R version 2.15.2 > > > What's the problem here? > > thanks! > > John > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thank you Paul! Can you please show me how to enable/install CytoscapeRPC? I am new to bioconductor, I simply installed graphite package with: source("http://bioconductor.org/biocLite.R") biocLite("graphite") Thanks, John ________________________________ From: Paul Shannon <pshannon@fhcrc.org> Cc: Paul Shannon <pshannon@fhcrc.org>; Bioconductor Mailing List <bioconductor@r-project.org> Sent: Monday, January 21, 2013 3:02 PM Subject: Re: [BioC] cytoscapePlot() from graphite package Hi John, This usually means that Cytoscape is not running, or that the CytoscapeRPC plugin is not enabled, or not enabled on the correct port. Let us know if you still have trouble after these things are set up. - Paul On Jan 21, 2013, at 2:58 PM, array chip wrote: > Hi, I was trying to use cytoscapePlot() from the graphite package, but got the error message below: > >> library(graphite) >> cytoscapePlot(convertIdentifiers(reactome$Unwinding of DNA, "symbol")) > Loading required package: RCytoscape > Loading required package: XMLRPC > Error in function (type, msg, asError = TRUE) : couldn't connect to host > In addition: Warning messages: > 1: package ‘RCytoscape’ was built under R version 2.15.2 > 2: package ‘XMLRPC’ was built under R version 2.15.2 > > > What's the problem here? > > thanks! > > John > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] ADD REPLY 0 Entering edit mode Hi John, To install the CytoscapeRPC plugin: 1) make sure that you have Cytoscape 2.8.3 installed 2) start Cytoscape 3) from the "Plugins" menu, choose "Manage Plugins" 4) Under "Communication/Scripting" (or maybe just "Scripting") locate CytoscapeRPC 5) Install, restart Cytoscape, then 6) From the plugins menu, choose CytoscapeRPC->Activate 7) You can also set CytoscapeRPC->Setting->Autostart Let me know if this works. - Paul On Jan 21, 2013, at 3:13 PM, array chip wrote: > Thank you Paul! Can you please show me how to enable/install CytoscapeRPC? I am new to bioconductor, I simply installed graphite package with: > > source("http://bioconductor.org/biocLite.R") > biocLite("graphite") > > > Thanks, > > John > > > > From: Paul Shannon <pshannon at="" fhcrc.org=""> > To: array chip <arrayprofile at="" yahoo.com=""> > Cc: Paul Shannon <pshannon at="" fhcrc.org="">; Bioconductor Mailing List <bioconductor at="" r-project.org=""> > Sent: Monday, January 21, 2013 3:02 PM > Subject: Re: [BioC] cytoscapePlot() from graphite package > > Hi John, > > This usually means that Cytoscape is not running, or that the CytoscapeRPC plugin is not enabled, or not enabled on the correct port. > > Let us know if you still have trouble after these things are set up. > > - Paul > > > > On Jan 21, 2013, at 2:58 PM, array chip wrote: > > > Hi, I was trying to use cytoscapePlot() from the graphite package, but got the error message below: > > > >> library(graphite) > >> cytoscapePlot(convertIdentifiers(reactome$Unwinding of DNA, "symbol")) > > Loading required package: RCytoscape > > Loading required package: XMLRPC > > Error in function (type, msg, asError = TRUE) : couldn't connect to host > > In addition: Warning messages: > > 1: package ?RCytoscape? was built under R version 2.15.2 > > 2: package ?XMLRPC? was built under R version 2.15.2 > > > > > > What's the problem here? > > > > thanks! > > > > John > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >
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Hi Paul, thanks very much for the details. I figured out from your RCytoscape manual as well! John ________________________________ From: Paul Shannon <pshannon@fhcrc.org> Cc: Paul Shannon <pshannon@fhcrc.org>; Bioconductor Mailing List <bioconductor@r-project.org> Sent: Monday, January 21, 2013 3:26 PM Subject: Re: [BioC] cytoscapePlot() from graphite package Hi John, To install the CytoscapeRPC plugin: Â  1) make sure that you have Cytoscape 2.8.3 installed Â  2) start Cytoscape Â  3) from the "Plugins" menu, choose "Manage Plugins" Â  4) Under "Communication/Scripting" (or maybe just "Scripting") locate CytoscapeRPC Â  5) Install, restart Cytoscape, then Â  6) From the plugins menu, choose CytoscapeRPC->Activate Â  7) You can also set CytoscapeRPC->Setting->Autostart Let me know if this works. - Paul On Jan 21, 2013, at 3:13 PM, array chip wrote: > Thank you Paul! Can you please show me how to enable/install CytoscapeRPC? I am new to bioconductor, I simply installed graphite package with: > > source("http://bioconductor.org/biocLite.R") > biocLite("graphite") > > > Thanks, > > John > > > > From: Paul Shannon <pshannon@fhcrc.org> > Cc: Paul Shannon <pshannon@fhcrc.org>; Bioconductor Mailing List <bioconductor@r-project.org> > Sent: Monday, January 21, 2013 3:02 PM > Subject: Re: [BioC] cytoscapePlot() from graphite package > > Hi John, > > This usually means that Cytoscape is not running, or that the CytoscapeRPC plugin is not enabled, or not enabled on the correct port. > > Let us know if you still have trouble after these things are set up. > > - Paul > > > > On Jan 21, 2013, at 2:58 PM, array chip wrote: > > > Hi, I was trying to use cytoscapePlot() from the graphite package, but got the error message below: > > > >> library(graphite) > >> cytoscapePlot(convertIdentifiers(reactome\$Unwinding of DNA, "symbol")) > > Loading required package: RCytoscape > > Loading required package: XMLRPC > > Error in function (type, msg, asError = TRUE)Â  : couldn't connect to host > > In addition: Warning messages: > > 1: package âRCytoscapeâ was built under R version 2.15.2 > > 2: package âXMLRPCâ was built under R version 2.15.2 > > > > > > What's the problem here? > > > > thanks! > > > > John > >Â  Â  [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]
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hu duan ▴ 30
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