{"issue":{"created_at":"2011-11-26T20:11:16Z","state":"open","updated_at":"2011-12-02T16:41:13Z","comments":5,"user":{"gravatar_id":"59f37362f734052e986709aaadc0943e","id":1211654,"url":"https://api.github.com/users/horowitzamir","avatar_url":"https://secure.gravatar.com/avatar/59f37362f734052e986709aaadc0943e?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","login":"horowitzamir"},"body":"Hi all,\r\n\r\nI was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:\r\n\r\nLoading required package: igraph\r\nLoading required package: methods\r\nScalable Robust Estimators with High Breakdown Point (version 1.3-01)\r\nError in FUN(X[[1L]], ...) : \r\n  Panel files must be a subset of analysis files\r\nCalls: SPADE.driver -> lapply -> FUN\r\nExecution halted\r\n\r\nThis has been working fine for me since installing the program, but suddenly I received the above message. I have tried restarting my computer, but unfortunately, this did not correct it.\r\n\r\nThanks very much.\r\n\r\nAmir","assignee":null,"id":2356769,"labels":[],"number":16,"pull_request":{"patch_url":null,"html_url":null,"diff_url":null},"title":"SPADE plugin not working","closed_at":null,"html_url":"https://github.com/nolanlab/spade/issues/16","url":"https://api.github.com/repos/nolanlab/spade/issues/16","milestone":null},"action":"created","comment":{"created_at":"2011-12-02T16:41:12Z","updated_at":"2011-12-02T16:41:12Z","user":{"gravatar_id":"59f37362f734052e986709aaadc0943e","id":1211654,"url":"https://api.github.com/users/horowitzamir","avatar_url":"https://secure.gravatar.com/avatar/59f37362f734052e986709aaadc0943e?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png","login":"horowitzamir"},"body":"Hi Erin, \n\n\nHope this finds you well. I have been getting much more comfortable navigating the SPADE program. As it turns out, my boss is color blind w.r.t. reds and greens. Is there any chance that there is some way to change the color scale within cityscape? \n\n\nI realize that this may be a long shot. If you have any suggestions, I would be very appreciative. \n\n\nAll my best \n\n\nAmir \n\n\n\n\n\n_________________ Amir Horowitz, PhD \nPostdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine \nFairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 \n----- Original Message -----\nFrom: \"Erin Simonds\" <reply@reply.github.com> \nTo: \"horowitzamir\" <amirh@stanford.edu> \nSent: Tuesday, November 29, 2011 11:40:07 AM \nSubject: Re: [spade] SPADE plugin not working (#16) \n\nHi Amir, \n\nGating: No, not yet. This is planned for mid-2012. \n\nStatistics: If you select a group of nodes, and choose \"Node Attribute \nBrowser\" at the bottom of the screen. You can click the \"Select \nattributes\" button (see attached) to display median and CV values for the \nnodes. \n\nAlso, if you select a group of nodes, Cytoscape performs a T-test to tell \nyou how that group of nodes is 'significantly different' from the rest of \nthe tree. This tells you what markers were important in defining those \nclusters. The Development version of the Cytoscape plugin displays this \ninformation in a more friendly table. You can download it here: \nhttps://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true \n\n- Erin \n\n\n\nOn Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < \nreply@reply.github.com \n> wrote: \n\n> Hi Erin, \n> \n> \n> First off, thanks very much for the help with getting the bug worked out. \n> The cityscape is working beautiful right now. I was, however, wondering if \n> it is possible to draw gates and generate statistics within the cityscape \n> program. Could you please confirm or disconfirm this for me? \n> \n> \n> Thanks again \n> \n> \n> best wishes \n> \n> \n> Amir \n> \n> \n> \n> \n> \n> _________________ Amir Horowitz, PhD \n> Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory \n> / Stanford University School of Medicine \n> Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA \n> 94305-5126 \n> ----- Original Message ----- \n> From: \"Erin Simonds\" <reply@reply.github.com> \n> To: \"horowitzamir\" <amirh@stanford.edu> \n> Sent: Saturday, November 26, 2011 12:27:43 PM \n> Subject: Re: [spade] SPADE plugin not working (#16) \n> \n> This usually means that there is a disagreement between the files in the \n> folder you are analyzing, and the runSPADE.R file. Perhaps you moved an \n> FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? \n> If you don't feel like troubleshooting, you should be able to fix the \n> problem by setting up a new analysis from the beginning in the Cytoscape \n> interface. Post back here if you still have trouble. \n> \n> \n> \n> On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < \n> reply@reply.github.com \n> > wrote: \n> \n> > Hi all, \n> > \n> > I was wondering if anyone has seen the following error message before \n> > while trying to run the SPADE plugin: \n> > \n> > Loading required package: igraph \n> > Loading required package: methods \n> > Scalable Robust Estimators with High Breakdown Point (version 1.3-01) \n> > Error in FUN(X[[1L]], ...) : \n> > Panel files must be a subset of analysis files \n> > Calls: SPADE.driver -> lapply -> FUN \n> > Execution halted \n> > \n> > This has been working fine for me since installing the program, but \n> > suddenly I received the above message. I have tried restarting my \n> computer, \n> > but unfortunately, this did not correct it. \n> > \n> > Thanks very much. \n> > \n> > Amir \n> > \n> > --- \n> > Reply to this email directly or view it on GitHub: \n> > https://github.com/nolanlab/spade/issues/16 \n> > \n> \n> --- \n> Reply to this email directly or view it on GitHub: \n> https://github.com/nolanlab/spade/issues/16#issuecomment-2883695 \n> \n> --- \n> Reply to this email directly or view it on GitHub: \n> https://github.com/nolanlab/spade/issues/16#issuecomment-2931428 \n> \n\n--- \nReply to this email directly or view it on GitHub: \nhttps://github.com/nolanlab/spade/issues/16#issuecomment-2943933","id":2992414,"url":"https://api.github.com/repos/nolanlab/spade/issues/comments/2992414"}}