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SPADE: Spanning Tree Progression of Density Normalized Events
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SPADE plugin not working #16

Closed horowitzamir closed 12 years ago

horowitzamir commented 12 years ago

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

esimonds commented 12 years ago

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

horowitzamir commented 12 years ago

Thanks very much, Erin. Really great of you to get back to me so promptly.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

horowitzamir commented 12 years ago

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

esimonds commented 12 years ago

Hi Amir,

Gating: No, not yet. This is planned for mid-2012.

Statistics: If you select a group of nodes, and choose "Node Attribute Browser" at the bottom of the screen. You can click the "Select attributes" button (see attached) to display median and CV values for the nodes.

Also, if you select a group of nodes, Cytoscape performs a T-test to tell you how that group of nodes is 'significantly different' from the rest of the tree. This tells you what markers were important in defining those clusters. The Development version of the Cytoscape plugin displays this information in a more friendly table. You can download it here: https://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true

On Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2931428

horowitzamir commented 12 years ago

Hi Erin,

Hope 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?

I realize that this may be a long shot. If you have any suggestions, I would be very appreciative.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Tuesday, November 29, 2011 11:40:07 AM Subject: Re: [spade] SPADE plugin not working (#16)

Hi Amir,

Gating: No, not yet. This is planned for mid-2012.

Statistics: If you select a group of nodes, and choose "Node Attribute Browser" at the bottom of the screen. You can click the "Select attributes" button (see attached) to display median and CV values for the nodes.

Also, if you select a group of nodes, Cytoscape performs a T-test to tell you how that group of nodes is 'significantly different' from the rest of the tree. This tells you what markers were important in defining those clusters. The Development version of the Cytoscape plugin displays this information in a more friendly table. You can download it here: https://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true

On Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2931428

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2943933

esimonds commented 12 years ago

Great question. The answer is yes and no ... You can go to the VizMapper plugin and change the scale for a single plot to grayscale or yellow/blue but this will be lost when you switch to another file.

Alternatively you can force a different color scale in the Produce PDFs feature. That's not as straightforward but I can help you with it if you like.

In a few months this feature will be built in to the interface.

On a bit of a different note, most red/green colorblind folks can differentiate red and blue, which are the extremes of the default color scale. But I am sensitive to this issue (we have an RG colorblind person in our lab) and I realize it varies from person to person. Has your boss reported difficulty seeing the default tree colors?

Thanks for the feedback!

Sent from my iPhone

On Dec 2, 2011, at 8:41 AM, horowitzamir reply@reply.github.com wrote:

Hi Erin,

Hope 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?

I realize that this may be a long shot. If you have any suggestions, I would be very appreciative.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Tuesday, November 29, 2011 11:40:07 AM Subject: Re: [spade] SPADE plugin not working (#16)

Hi Amir,

Gating: No, not yet. This is planned for mid-2012.

Statistics: If you select a group of nodes, and choose "Node Attribute Browser" at the bottom of the screen. You can click the "Select attributes" button (see attached) to display median and CV values for the nodes.

Also, if you select a group of nodes, Cytoscape performs a T-test to tell you how that group of nodes is 'significantly different' from the rest of the tree. This tells you what markers were important in defining those clusters. The Development version of the Cytoscape plugin displays this information in a more friendly table. You can download it here: https://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true

  • Erin

On Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2931428

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2943933

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2992414

horowitzamir commented 12 years ago

Thanks so much for the great feedback, Erin. Actually, next Tuesday, when I have my lab meeting, will be the first time that my boss ever sees this data. I'm quite positive that he saw your group's Science publication, but I have never really discussed this issue with him.

I will definitely try out your suggestions though.

Thanks again

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Friday, December 2, 2011 10:28:50 AM Subject: Re: [spade] SPADE plugin not working (#16)

Great question. The answer is yes and no ... You can go to the VizMapper plugin and change the scale for a single plot to grayscale or yellow/blue but this will be lost when you switch to another file.

Alternatively you can force a different color scale in the Produce PDFs feature. That's not as straightforward but I can help you with it if you like.

In a few months this feature will be built in to the interface.

On a bit of a different note, most red/green colorblind folks can differentiate red and blue, which are the extremes of the default color scale. But I am sensitive to this issue (we have an RG colorblind person in our lab) and I realize it varies from person to person. Has your boss reported difficulty seeing the default tree colors?

Thanks for the feedback!

Sent from my iPhone

On Dec 2, 2011, at 8:41 AM, horowitzamir reply@reply.github.com wrote:

Hi Erin,

Hope 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?

I realize that this may be a long shot. If you have any suggestions, I would be very appreciative.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Tuesday, November 29, 2011 11:40:07 AM Subject: Re: [spade] SPADE plugin not working (#16)

Hi Amir,

Gating: No, not yet. This is planned for mid-2012.

Statistics: If you select a group of nodes, and choose "Node Attribute Browser" at the bottom of the screen. You can click the "Select attributes" button (see attached) to display median and CV values for the nodes.

Also, if you select a group of nodes, Cytoscape performs a T-test to tell you how that group of nodes is 'significantly different' from the rest of the tree. This tells you what markers were important in defining those clusters. The Development version of the Cytoscape plugin displays this information in a more friendly table. You can download it here: https://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true

  • Erin

On Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2931428

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2943933

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2992414

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2993780

horowitzamir commented 12 years ago

Hi Erin,

So, I met today with one of my lab members who does some computer programming on the side. He helped me try to install that 'developers'" version of cytoSPADE in order to get access to the more user-friendly tables. We were unsuccessful in installing the plug-in. He told me that it was most likely reflective of a bug, either in the plug-in or in the cityscape package. Could you please confirm for me that the link you provided downloads the appropriate and compatible plug-in which you intended for me to have?

Thanks very much. I hope you have a great weekend.

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Friday, December 2, 2011 10:28:50 AM Subject: Re: [spade] SPADE plugin not working (#16)

Great question. The answer is yes and no ... You can go to the VizMapper plugin and change the scale for a single plot to grayscale or yellow/blue but this will be lost when you switch to another file.

Alternatively you can force a different color scale in the Produce PDFs feature. That's not as straightforward but I can help you with it if you like.

In a few months this feature will be built in to the interface.

On a bit of a different note, most red/green colorblind folks can differentiate red and blue, which are the extremes of the default color scale. But I am sensitive to this issue (we have an RG colorblind person in our lab) and I realize it varies from person to person. Has your boss reported difficulty seeing the default tree colors?

Thanks for the feedback!

Sent from my iPhone

On Dec 2, 2011, at 8:41 AM, horowitzamir reply@reply.github.com wrote:

Hi Erin,

Hope 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?

I realize that this may be a long shot. If you have any suggestions, I would be very appreciative.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Tuesday, November 29, 2011 11:40:07 AM Subject: Re: [spade] SPADE plugin not working (#16)

Hi Amir,

Gating: No, not yet. This is planned for mid-2012.

Statistics: If you select a group of nodes, and choose "Node Attribute Browser" at the bottom of the screen. You can click the "Select attributes" button (see attached) to display median and CV values for the nodes.

Also, if you select a group of nodes, Cytoscape performs a T-test to tell you how that group of nodes is 'significantly different' from the rest of the tree. This tells you what markers were important in defining those clusters. The Development version of the Cytoscape plugin displays this information in a more friendly table. You can download it here: https://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true

  • Erin

On Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2883695

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2931428

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2943933

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2992414

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16#issuecomment-2993780

esimonds commented 12 years ago

Hi Amir,

Here are the steps:

1) Download CytoSPADE.jar from the link I sent before 2) In Finder, open /Applications/Cytoscape_v2.8.2/plugins 3) Copy CytoSPADE.jar to the plugins folder 4) Quit and re-open Cytoscape

Let me know how that goes. If you have an error message, please send a screenshot.

Thanks,

Erin

On Fri, Dec 2, 2011 at 4:13 PM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

So, I met today with one of my lab members who does some computer programming on the side. He helped me try to install that 'developers'" version of cytoSPADE in order to get access to the more user-friendly tables. We were unsuccessful in installing the plug-in. He told me that it was most likely reflective of a bug, either in the plug-in or in the cityscape package. Could you please confirm for me that the link you provided downloads the appropriate and compatible plug-in which you intended for me to have?

Thanks very much. I hope you have a great weekend.

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Friday, December 2, 2011 10:28:50 AM Subject: Re: [spade] SPADE plugin not working (#16)

Great question. The answer is yes and no ... You can go to the VizMapper plugin and change the scale for a single plot to grayscale or yellow/blue but this will be lost when you switch to another file.

Alternatively you can force a different color scale in the Produce PDFs feature. That's not as straightforward but I can help you with it if you like.

In a few months this feature will be built in to the interface.

On a bit of a different note, most red/green colorblind folks can differentiate red and blue, which are the extremes of the default color scale. But I am sensitive to this issue (we have an RG colorblind person in our lab) and I realize it varies from person to person. Has your boss reported difficulty seeing the default tree colors?

Thanks for the feedback!

Sent from my iPhone

On Dec 2, 2011, at 8:41 AM, horowitzamir reply@reply.github.com wrote:

Hi Erin,

Hope 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?

I realize that this may be a long shot. If you have any suggestions, I would be very appreciative.

All my best

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Tuesday, November 29, 2011 11:40:07 AM Subject: Re: [spade] SPADE plugin not working (#16)

Hi Amir,

Gating: No, not yet. This is planned for mid-2012.

Statistics: If you select a group of nodes, and choose "Node Attribute Browser" at the bottom of the screen. You can click the "Select attributes" button (see attached) to display median and CV values for the nodes.

Also, if you select a group of nodes, Cytoscape performs a T-test to tell you how that group of nodes is 'significantly different' from the rest of the tree. This tells you what markers were important in defining those clusters. The Development version of the Cytoscape plugin displays this information in a more friendly table. You can download it here:

https://github.com/nolanlab/spade/blob/dev/inst/tools/CytoSPADE.jar?raw=true

  • Erin

On Tue, Nov 29, 2011 at 7:35 AM, horowitzamir < reply@reply.github.com

wrote:

Hi Erin,

First off, thanks very much for the help with getting the bug worked out. The cityscape is working beautiful right now. I was, however, wondering if it is possible to draw gates and generate statistics within the cityscape program. Could you please confirm or disconfirm this for me?

Thanks again

best wishes

Amir

_____ Amir Horowitz, PhD Postdoctoral Fellow / Department of Structural Biology / Parham Laboratory / Stanford University School of Medicine Fairchild Bldg / Room D100 / 299 Campus Drive West / Stanford, CA 94305-5126 ----- Original Message ----- From: "Erin Simonds" reply@reply.github.com To: "horowitzamir" amirh@stanford.edu Sent: Saturday, November 26, 2011 12:27:43 PM Subject: Re: [spade] SPADE plugin not working (#16)

This usually means that there is a disagreement between the files in the folder you are analyzing, and the runSPADE.R file. Perhaps you moved an FCS file, or renamed one? Maybe you edited the runSPADE.R file by hand? If you don't feel like troubleshooting, you should be able to fix the problem by setting up a new analysis from the beginning in the Cytoscape interface. Post back here if you still have trouble.

On Sat, Nov 26, 2011 at 12:11 PM, horowitzamir < reply@reply.github.com

wrote:

Hi all,

I was wondering if anyone has seen the following error message before while trying to run the SPADE plugin:

Loading required package: igraph Loading required package: methods Scalable Robust Estimators with High Breakdown Point (version 1.3-01) Error in FUN(X[[1L]], ...) : Panel files must be a subset of analysis files Calls: SPADE.driver -> lapply -> FUN Execution halted

This 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.

Thanks very much.

Amir

Reply to this email directly or view it on GitHub: https://github.com/nolanlab/spade/issues/16

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mlinderm commented 12 years ago

I am closing this issue, please re-open if you are still having issues...